td: td.py annotate

annotate td.py @ 0:3e56058d9552 draft default tip

planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty

author	mheinzl
date	Wed, 16 Oct 2019 04:17:59 -0400
parents
children

rev	line source
0 3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1 #!/usr/bin/env python
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	2
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	3 # Tag distance analysis of SSCSs
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	4 #
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	5 # Author: Monika Heinzl, Johannes-Kepler University Linz (Austria)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	6 # Contact: monika.heinzl@edumail.at
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	7 #
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	8 # Takes at least one TABULAR file with tags before the alignment to the SSCS and
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	9 # optionally a second TABULAR file as input. The program produces a plot which shows a histogram of Hamming distances
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	10 # separated after family sizes, a family size distribution separated after Hamming distances for all (sample_size=0)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	11 # or a given sample of SSCSs or SSCSs, which form a DCS. In additon, the tool produces HD and FSD plots for the
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	12 # difference between the HDs of both parts of the tags and for the chimeric reads and finally a CSV file with the
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	13 # data of the plots. It is also possible to perform the HD analysis with shortened tags with given sizes as input.
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	14 # The tool can run on a certain number of processors, which can be defined by the user.
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	15
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	16 # USAGE: python td.py --inputFile filename --inputName1 filename --sample_size int /
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	17 # --only_DCS True --FamilySize3 True --subset_tag True --nproc int --minFS int --maxFS int
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	18 # --nr_above_bars True/False --output_tabular outptufile_name_tabular
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	19
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	20 import argparse
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	21 import itertools
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	22 import operator
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	23 import sys
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	24 from collections import Counter, defaultdict
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	25 from functools import partial
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	26 from multiprocessing.pool import Pool
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	27 import random
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	28 import os
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	29
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	30 import matplotlib.pyplot as plt
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	31 import numpy
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	32 from matplotlib.backends.backend_pdf import PdfPages
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	33
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	34 plt.switch_backend('agg')
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	35
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	36
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	37 def plotFSDwithHD2(familySizeList1, maximumXFS, minimumXFS, originalCounts,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	38 subtitle, pdf, relative=False, diff=True, rel_freq=False):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	39 if diff is False:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	40 colors = ["#e6194b", "#3cb44b", "#ffe119", "#0082c8", "#f58231", "#911eb4"]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	41 labels = ["TD=1", "TD=2", "TD=3", "TD=4", "TD=5-8", "TD>8"]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	42 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	43 colors = ["#93A6AB", "#403C14", "#731E41", "#BAB591", "#085B6F", "#E8AA35", "#726C66"]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	44 if relative is True:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	45 labels = ["d=0", "d=0.1", "d=0.2", "d=0.3", "d=0.4", "d=0.5-0.8", "d>0.8"]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	46 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	47 labels = ["d=0", "d=1", "d=2", "d=3", "d=4", "d=5-8", "d>8"]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	48
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	49 fig = plt.figure(figsize=(6, 7))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	50 ax = fig.add_subplot(111)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	51 plt.subplots_adjust(bottom=0.1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	52 p1 = numpy.bincount(numpy.concatenate(familySizeList1))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	53 maximumY = numpy.amax(p1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	54
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	55 if len(range(minimumXFS, maximumXFS)) == 0:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	56 range1 = range(minimumXFS - 1, minimumXFS + 2)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	57 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	58 range1 = range(0, maximumXFS + 2)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	59
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	60 if rel_freq:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	61 w = [numpy.zeros_like(data) + 1. / len(numpy.concatenate(familySizeList1)) for data in familySizeList1]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	62 counts = plt.hist(familySizeList1, label=labels, weights=w, color=colors, stacked=True,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	63 rwidth=0.8, alpha=1, align="left", edgecolor="None", bins=range1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	64 plt.ylabel("Relative Frequency", fontsize=14)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	65 plt.ylim((0, 1.07))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	66 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	67 counts = plt.hist(familySizeList1, label=labels, color=colors, stacked=True,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	68 rwidth=0.8, alpha=1, align="left", edgecolor="None", bins=range1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	69 if len(numpy.concatenate(familySizeList1)) != 0:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	70 plt.ylim((0, max(numpy.bincount(numpy.concatenate(familySizeList1))) * 1.1))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	71 plt.ylabel("Absolute Frequency", fontsize=14)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	72 plt.ylim((0, maximumY * 1.2))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	73 plt.legend(loc='upper right', fontsize=14, frameon=True, bbox_to_anchor=(1.45, 1))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	74 plt.suptitle(subtitle, y=1, x=0.5, fontsize=14)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	75 plt.xlabel("Family size", fontsize=14)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	76 ticks = numpy.arange(0, maximumXFS + 1, 1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	77 ticks1 = map(str, ticks)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	78 if maximumXFS >= 20:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	79 ticks1[len(ticks1) - 1] = ">=20"
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	80 plt.xticks(numpy.array(ticks), ticks1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	81 [l.set_visible(False) for (i, l) in enumerate(ax.get_xticklabels()) if i % 5 != 0]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	82 plt.xlim((0, maximumXFS + 1))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	83 legend = "\nfamily size: \nabsolute frequency: \nrelative frequency: "
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	84 plt.text(0.15, -0.08, legend, size=12, transform=plt.gcf().transFigure)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	85
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	86 count = numpy.bincount(originalCounts) # original counts
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	87 if max(originalCounts) >= 20:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	88 max_count = ">= 20"
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	89 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	90 max_count = max(originalCounts)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	91 legend1 = "{}\n{}\n{:.5f}".format(max_count, p1[len(p1) - 1], float(p1[len(p1) - 1]) / sum(p1))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	92 plt.text(0.5, -0.08, legend1, size=12, transform=plt.gcf().transFigure)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	93 legend3 = "singletons\n{:,}\n{:.5f}".format(int(p1[1]), float(p1[1]) / sum(p1))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	94 plt.text(0.7, -0.08, legend3, transform=plt.gcf().transFigure, size=12)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	95 plt.grid(b=True, which='major', color='#424242', linestyle=':')
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	96 pdf.savefig(fig, bbox_inches="tight")
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	97 plt.close("all")
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	98
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	99
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	100 def plotHDwithFSD(list1, maximumX, minimumX, subtitle, lenTags, pdf, xlabel, relative=False,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	101 nr_above_bars=True, nr_unique_chimeras=0, len_sample=0, rel_freq=False):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	102 if relative is True:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	103 step = 0.1
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	104 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	105 step = 1
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	106
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	107 fig = plt.figure(figsize=(6, 8))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	108 plt.subplots_adjust(bottom=0.1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	109 p1 = numpy.array([v for k, v in sorted(Counter(numpy.concatenate(list1)).iteritems())])
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	110 maximumY = numpy.amax(p1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	111 if relative is True: # relative difference
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	112 bin1 = numpy.arange(-1, maximumX + 0.2, 0.1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	113 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	114 bin1 = maximumX + 1
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	115
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	116 if rel_freq:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	117 w = [numpy.zeros_like(data) + 1. / len(numpy.concatenate(list1)) for data in list1]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	118 counts = plt.hist(list1, bins=bin1, edgecolor='black', linewidth=1, weights=w,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	119 label=["FS=1", "FS=2", "FS=3", "FS=4", "FS=5-10", "FS>10"], rwidth=0.8,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	120 color=["#808080", "#FFFFCC", "#FFBF00", "#DF0101", "#0431B4", "#86B404"],
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	121 stacked=True, alpha=1, align="left", range=(0, maximumX + 1))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	122 plt.ylim((0, 1.07))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	123 plt.ylabel("Relative Frequency", fontsize=14)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	124 bins = counts[1] # width of bins
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	125 counts = numpy.array(map(float, counts[0][5]))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	126
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	127 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	128 counts = plt.hist(list1, bins=bin1, edgecolor='black', linewidth=1,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	129 label=["FS=1", "FS=2", "FS=3", "FS=4", "FS=5-10", "FS>10"], rwidth=0.8,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	130 color=["#808080", "#FFFFCC", "#FFBF00", "#DF0101", "#0431B4", "#86B404"],
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	131 stacked=True, alpha=1, align="left", range=(0, maximumX + 1))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	132 maximumY = numpy.amax(p1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	133 plt.ylim((0, maximumY * 1.2))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	134 plt.ylabel("Absolute Frequency", fontsize=14)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	135 bins = counts[1] # width of bins
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	136 counts = numpy.array(map(int, counts[0][5]))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	137
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	138 plt.legend(loc='upper right', fontsize=14, frameon=True, bbox_to_anchor=(1.45, 1))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	139 plt.suptitle(subtitle, y=1, x=0.5, fontsize=14)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	140 plt.xlabel(xlabel, fontsize=14)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	141 plt.grid(b=True, which='major', color='#424242', linestyle=':')
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	142 plt.xlim((minimumX - step, maximumX + step))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	143 # plt.axis((minimumX - step, maximumX + step, 0, numpy.amax(counts) + sum(counts) * 0.1))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	144 plt.xticks(numpy.arange(0, maximumX + step, step))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	145
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	146 if nr_above_bars:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	147 bin_centers = -0.4 * numpy.diff(bins) + bins[:-1]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	148 for x_label, label in zip(counts, bin_centers): # labels for values
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	149 if x_label == 0:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	150 continue
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	151 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	152 if rel_freq:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	153 plt.annotate("{:,}\n{:.3f}".format(int(round(x_label * len(numpy.concatenate(list1)))),
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	154 float(x_label)),
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	155 xy=(label, x_label + len(numpy.concatenate(list1)) * 0.0001),
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	156 xycoords="data", color="#000066", fontsize=10)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	157 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	158 plt.annotate("{:,}\n{:.3f}".format(x_label, float(x_label) / sum(counts)),
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	159 xy=(label, x_label + len(numpy.concatenate(list1)) * 0.01),
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	160 xycoords="data", color="#000066", fontsize=10)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	161
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	162 if nr_unique_chimeras != 0:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	163 if (relative and ((counts[len(counts)-1] / nr_unique_chimeras) == 2)) or \
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	164 (sum(counts) / nr_unique_chimeras) == 2:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	165 legend = "nr. of tags = {:,}\nsample size = {:,}\nnr. of data points = {:,}\nnr. of CF = {:,} ({:,})"\
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	166 .format(lenTags, len_sample, len(numpy.concatenate(list1)), nr_unique_chimeras, nr_unique_chimeras * 2)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	167 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	168 legend = "nr. of tags = {:,}\nsample size = {:,}\nnr. of data points = {:,}\nnr. of CF = {:,}".format(
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	169 lenTags, len_sample, len(numpy.concatenate(list1)), nr_unique_chimeras)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	170 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	171 legend = "nr. of tags = {:,}\nsample size = {:,}\nnr. of data points = {:,}".format(
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	172 lenTags, len_sample, len(numpy.concatenate(list1)))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	173
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	174 plt.text(0.14, -0.07, legend, size=12, transform=plt.gcf().transFigure)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	175 pdf.savefig(fig, bbox_inches="tight")
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	176 plt.close("all")
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	177 plt.clf()
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	178
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	179
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	180 def plotHDwithDCS(list1, maximumX, minimumX, subtitle, lenTags, pdf, xlabel, relative=False,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	181 nr_above_bars=True, nr_unique_chimeras=0, len_sample=0, rel_freq=False):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	182 step = 1
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	183 fig = plt.figure(figsize=(6, 8))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	184 plt.subplots_adjust(bottom=0.1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	185 p1 = numpy.array([v for k, v in sorted(Counter(numpy.concatenate(list1)).iteritems())])
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	186 maximumY = numpy.amax(p1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	187 bin1 = maximumX + 1
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	188 if rel_freq:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	189 w = [numpy.zeros_like(data) + 1. / len(numpy.concatenate(list1)) for data in list1]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	190 counts = plt.hist(list1, bins=bin1, edgecolor='black', linewidth=1, weights=w,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	191 label=["DCS", "ab", "ba"], rwidth=0.8, color=["#FF0000", "#5FB404", "#FFBF00"],
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	192 stacked=True, alpha=1, align="left", range=(0, maximumX + 1))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	193 plt.ylim((0, 1.07))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	194 plt.ylabel("Relative Frequency", fontsize=14)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	195 bins = counts[1] # width of bins
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	196 counts = numpy.array(map(float, counts[0][2]))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	197
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	198 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	199 counts = plt.hist(list1, bins=bin1, edgecolor='black', linewidth=1,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	200 label=["DCS", "ab", "ba"], rwidth=0.8, color=["#FF0000", "#5FB404", "#FFBF00"],
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	201 stacked=True, alpha=1, align="left", range=(0, maximumX + 1))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	202 plt.ylim((0, maximumY * 1.2))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	203 plt.ylabel("Absolute Frequency", fontsize=14)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	204 bins = counts[1] # width of bins
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	205 counts = numpy.array(map(int, counts[0][2]))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	206
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	207 plt.legend(loc='upper right', fontsize=14, frameon=True, bbox_to_anchor=(1.45, 1))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	208 plt.suptitle(subtitle, y=1, x=0.5, fontsize=14)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	209 plt.xlabel(xlabel, fontsize=14)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	210 plt.grid(b=True, which='major', color='#424242', linestyle=':')
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	211 plt.xlim((minimumX - step, maximumX + step))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	212 # plt.axis((minimumX - step, maximumX + step, 0, numpy.amax(counts) + sum(counts) * 0.1))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	213 plt.xticks(numpy.arange(0, maximumX + step, step))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	214
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	215 if nr_above_bars:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	216 bin_centers = -0.4 * numpy.diff(bins) + bins[:-1]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	217 for x_label, label in zip(counts, bin_centers): # labels for values
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	218 if x_label == 0:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	219 continue
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	220 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	221 if rel_freq:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	222 plt.annotate("{:,}\n{:.3f}".format(int(round(x_label * len(numpy.concatenate(list1)))),
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	223 float(x_label)),
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	224 xy=(label, x_label + len(numpy.concatenate(list1)) * 0.0001),
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	225 xycoords="data", color="#000066", fontsize=10)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	226 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	227 plt.annotate("{:,}\n{:.3f}".format(x_label, float(x_label) / sum(counts)),
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	228 xy=(label, x_label + len(numpy.concatenate(list1)) * 0.01),
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	229 xycoords="data", color="#000066", fontsize=10)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	230
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	231 if nr_unique_chimeras != 0:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	232 if (sum(counts) / nr_unique_chimeras) == 2:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	233 legend = "nr. of tags = {:,}\nsample size = {:,}\nnr. of data points = {:,}\nnr. of CF = {:,} ({:,})".\
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	234 format(lenTags, len_sample, len(numpy.concatenate(list1)), nr_unique_chimeras, nr_unique_chimeras * 2)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	235 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	236 legend = "nr. of tags = {:,}\nsample size = {:,}\nnr. of data points = {:,}\nnr. of CF = {:,}".format(
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	237 lenTags, len_sample, len(numpy.concatenate(list1)), nr_unique_chimeras)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	238 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	239 legend = "nr. of tags = {:,}\nsample size = {:,}\nnr. of data points = {:,}".format(
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	240 lenTags, len_sample, len(numpy.concatenate(list1)))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	241 plt.text(0.14, -0.07, legend, size=12, transform=plt.gcf().transFigure)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	242
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	243 legend2 = "SSCS ab = {:,} ({:.5f})\nSSCS ba = {:,} ({:.5f})\nDCS = {:,} ({:.5f})".format(
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	244 len(list1[1]), len(list1[1]) / float(nr_unique_chimeras),
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	245 len(list1[2]), len(list1[2]) / float(nr_unique_chimeras),
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	246 len(list1[0]), len(list1[0]) / float(nr_unique_chimeras))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	247 plt.text(0.6, -0.047, legend2, size=12, transform=plt.gcf().transFigure)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	248
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	249 pdf.savefig(fig, bbox_inches="tight")
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	250 plt.close("all")
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	251 plt.clf()
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	252
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	253
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	254 def plotHDwithinSeq(sum1, sum1min, sum2, sum2min, min_value, lenTags, pdf, len_sample, rel_freq=False):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	255 fig = plt.figure(figsize=(6, 8))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	256 plt.subplots_adjust(bottom=0.1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	257
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	258 ham_partial = [sum1, sum1min, sum2, sum2min, numpy.array(min_value)] # new hd within tags
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	259 maximumX = numpy.amax(numpy.concatenate(ham_partial))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	260 minimumX = numpy.amin(numpy.concatenate(ham_partial))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	261 maximumY = numpy.amax(numpy.array(numpy.concatenate(map(lambda x: numpy.bincount(x), ham_partial))))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	262
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	263 if len(range(minimumX, maximumX)) == 0:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	264 range1 = minimumX
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	265 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	266 range1 = range(minimumX, maximumX + 2)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	267
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	268 if rel_freq:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	269 w = [numpy.zeros_like(data) + 1. / len(data) for data in ham_partial]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	270 plt.hist(ham_partial, align="left", rwidth=0.8, stacked=False, weights=w,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	271 label=["TD a.min", "TD b.max", "TD b.min", "TD a.max", "TD a.min + b.max,\nTD a.max + b.min"],
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	272 bins=range1, color=["#58ACFA", "#0404B4", "#FE642E", "#B40431", "#585858"],
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	273 edgecolor='black', linewidth=1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	274 plt.ylabel("Relative Frequency", fontsize=14)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	275 plt.ylim(0, 1.07)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	276 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	277 plt.hist(ham_partial, align="left", rwidth=0.8, stacked=False,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	278 label=["TD a.min", "TD b.max", "TD b.min", "TD a.max", "TD a.min + b.max,\nTD a.max + b.min"],
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	279 bins=range1, color=["#58ACFA", "#0404B4", "#FE642E", "#B40431", "#585858"],
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	280 edgecolor='black', linewidth=1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	281 plt.ylabel("Absolute Frequency", fontsize=14)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	282
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	283 plt.legend(loc='upper right', fontsize=14, frameon=True, bbox_to_anchor=(1.6, 1))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	284 plt.suptitle('Tag distances within tags', fontsize=14)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	285 plt.xlabel("TD", fontsize=14)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	286 plt.grid(b=True, which='major', color='#424242', linestyle=':')
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	287 plt.xlim((minimumX - 1, maximumX + 1))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	288 # plt.axis((minimumX - 1, maximumX + 1, 0, maximumY * 1.2))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	289 plt.xticks(numpy.arange(0, maximumX + 1, 1.0))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	290 legend = "nr. of tags = {:,}\nsample size = {:,}\nnr. of data points = {:,}".format(
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	291 lenTags, len_sample, len(numpy.concatenate(ham_partial)))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	292 plt.text(0.14, -0.05, legend, size=12, transform=plt.gcf().transFigure)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	293 pdf.savefig(fig, bbox_inches="tight")
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	294 plt.close("all")
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	295 plt.clf()
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	296
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	297
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	298 def createTableFSD2(list1, diff=True):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	299 selfAB = numpy.concatenate(list1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	300 uniqueFS = numpy.unique(selfAB)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	301 nr = numpy.arange(0, len(uniqueFS), 1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	302 if diff is False:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	303 count = numpy.zeros((len(uniqueFS), 6))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	304 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	305 count = numpy.zeros((len(uniqueFS), 7))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	306 state = 1
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	307 for i in list1:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	308 counts = list(Counter(i).items())
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	309 hd = [item[0] for item in counts]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	310 c = [item[1] for item in counts]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	311 table = numpy.column_stack((hd, c))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	312 if len(table) == 0:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	313 state = state + 1
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	314 continue
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	315 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	316 if state == 1:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	317 for k, l in zip(uniqueFS, nr):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	318 for j in table:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	319 if j[0] == uniqueFS[l]:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	320 count[l, 0] = j[1]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	321 if state == 2:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	322 for k, l in zip(uniqueFS, nr):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	323 for j in table:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	324 if j[0] == uniqueFS[l]:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	325 count[l, 1] = j[1]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	326 if state == 3:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	327 for k, l in zip(uniqueFS, nr):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	328 for j in table:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	329 if j[0] == uniqueFS[l]:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	330 count[l, 2] = j[1]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	331 if state == 4:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	332 for k, l in zip(uniqueFS, nr):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	333 for j in table:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	334 if j[0] == uniqueFS[l]:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	335 count[l, 3] = j[1]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	336 if state == 5:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	337 for k, l in zip(uniqueFS, nr):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	338 for j in table:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	339 if j[0] == uniqueFS[l]:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	340 count[l, 4] = j[1]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	341 if state == 6:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	342 for k, l in zip(uniqueFS, nr):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	343 for j in table:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	344 if j[0] == uniqueFS[l]:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	345 count[l, 5] = j[1]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	346 if state == 7:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	347 for k, l in zip(uniqueFS, nr):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	348 for j in table:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	349 if j[0] == uniqueFS[l]:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	350 count[l, 6] = j[1]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	351 state = state + 1
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	352 sumRow = count.sum(axis=1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	353 sumCol = count.sum(axis=0)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	354 uniqueFS = uniqueFS.astype(str)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	355 if uniqueFS[len(uniqueFS) - 1] == "20":
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	356 uniqueFS[len(uniqueFS) - 1] = ">20"
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	357 first = ["FS={}".format(i) for i in uniqueFS]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	358 final = numpy.column_stack((first, count, sumRow))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	359 return (final, sumCol)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	360
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	361
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	362 def createFileFSD2(summary, sumCol, overallSum, output_file, name, sep, rel=False, diff=True):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	363 output_file.write(name)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	364 output_file.write("\n")
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	365 if diff is False:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	366 output_file.write("{}TD=1{}TD=2{}TD=3{}TD=4{}TD=5-8{}TD>8{}sum{}\n".format(
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	367 sep, sep, sep, sep, sep, sep, sep, sep))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	368 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	369 if rel is False:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	370 output_file.write("{}diff=0{}diff=1{}diff=2{}diff=3{}diff=4{}diff=5-8{}diff>8{}sum{}\n".format(
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	371 sep, sep, sep, sep, sep, sep, sep, sep, sep))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	372 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	373 output_file.write("{}diff=0{}diff=0.1{}diff=0.2{}diff=0.3{}diff=0.4{}diff=0.5-0.8{}diff>0.8{}sum{}\n".
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	374 format(sep, sep, sep, sep, sep, sep, sep, sep, sep))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	375 for item in summary:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	376 for nr in item:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	377 if "FS" not in nr and "diff" not in nr:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	378 nr = nr.astype(float)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	379 nr = nr.astype(int)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	380 output_file.write("{}{}".format(nr, sep))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	381 output_file.write("\n")
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	382 output_file.write("sum{}".format(sep))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	383 sumCol = map(int, sumCol)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	384 for el in sumCol:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	385 output_file.write("{}{}".format(el, sep))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	386 output_file.write("{}{}".format(overallSum.astype(int), sep))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	387 output_file.write("\n\n")
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	388
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	389
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	390 def createTableHD(list1, row_label):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	391 selfAB = numpy.concatenate(list1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	392 uniqueHD = numpy.unique(selfAB)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	393 nr = numpy.arange(0, len(uniqueHD), 1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	394 count = numpy.zeros((len(uniqueHD), 6))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	395 state = 1
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	396 for i in list1:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	397 counts = list(Counter(i).items())
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	398 hd = [item[0] for item in counts]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	399 c = [item[1] for item in counts]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	400 table = numpy.column_stack((hd, c))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	401 if len(table) == 0:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	402 state = state + 1
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	403 continue
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	404 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	405 if state == 1:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	406 for k, l in zip(uniqueHD, nr):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	407 for j in table:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	408 if j[0] == uniqueHD[l]:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	409 count[l, 0] = j[1]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	410 if state == 2:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	411 for k, l in zip(uniqueHD, nr):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	412 for j in table:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	413 if j[0] == uniqueHD[l]:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	414 count[l, 1] = j[1]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	415 if state == 3:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	416 for k, l in zip(uniqueHD, nr):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	417 for j in table:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	418 if j[0] == uniqueHD[l]:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	419 count[l, 2] = j[1]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	420 if state == 4:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	421 for k, l in zip(uniqueHD, nr):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	422 for j in table:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	423 if j[0] == uniqueHD[l]:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	424 count[l, 3] = j[1]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	425 if state == 5:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	426 for k, l in zip(uniqueHD, nr):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	427 for j in table:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	428 if j[0] == uniqueHD[l]:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	429 count[l, 4] = j[1]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	430 if state == 6:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	431 for k, l in zip(uniqueHD, nr):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	432 for j in table:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	433 if j[0] == uniqueHD[l]:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	434 count[l, 5] = j[1]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	435 state = state + 1
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	436 sumRow = count.sum(axis=1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	437 sumCol = count.sum(axis=0)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	438 first = ["{}{}".format(row_label, i) for i in uniqueHD]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	439 final = numpy.column_stack((first, count, sumRow))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	440 return (final, sumCol)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	441
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	442
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	443 def createTableHDwithTags(list1):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	444 selfAB = numpy.concatenate(list1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	445 uniqueHD = numpy.unique(selfAB)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	446 nr = numpy.arange(0, len(uniqueHD), 1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	447 count = numpy.zeros((len(uniqueHD), 5))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	448 state = 1
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	449 for i in list1:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	450 counts = list(Counter(i).items())
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	451 hd = [item[0] for item in counts]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	452 c = [item[1] for item in counts]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	453 table = numpy.column_stack((hd, c))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	454 if len(table) == 0:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	455 state = state + 1
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	456 continue
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	457 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	458 if state == 1:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	459 for k, l in zip(uniqueHD, nr):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	460 for j in table:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	461 if j[0] == uniqueHD[l]:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	462 count[l, 0] = j[1]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	463 if state == 2:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	464 for k, l in zip(uniqueHD, nr):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	465 for j in table:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	466 if j[0] == uniqueHD[l]:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	467 count[l, 1] = j[1]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	468 if state == 3:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	469 for k, l in zip(uniqueHD, nr):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	470 for j in table:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	471 if j[0] == uniqueHD[l]:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	472 count[l, 2] = j[1]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	473 if state == 4:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	474 for k, l in zip(uniqueHD, nr):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	475 for j in table:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	476 if j[0] == uniqueHD[l]:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	477 count[l, 3] = j[1]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	478 if state == 5:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	479 for k, l in zip(uniqueHD, nr):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	480 for j in table:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	481 if j[0] == uniqueHD[l]:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	482 count[l, 4] = j[1]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	483 state = state + 1
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	484 sumRow = count.sum(axis=1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	485 sumCol = count.sum(axis=0)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	486 first = ["TD={}".format(i) for i in uniqueHD]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	487 final = numpy.column_stack((first, count, sumRow))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	488 return (final, sumCol)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	489
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	490
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	491 def createTableHDwithDCS(list1):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	492 selfAB = numpy.concatenate(list1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	493 uniqueHD = numpy.unique(selfAB)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	494 nr = numpy.arange(0, len(uniqueHD), 1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	495 count = numpy.zeros((len(uniqueHD), len(list1)))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	496 state = 1
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	497 for i in list1:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	498 counts = list(Counter(i).items())
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	499 hd = [item[0] for item in counts]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	500 c = [item[1] for item in counts]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	501 table = numpy.column_stack((hd, c))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	502 if len(table) == 0:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	503 state = state + 1
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	504 continue
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	505 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	506 if state == 1:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	507 for k, l in zip(uniqueHD, nr):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	508 for j in table:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	509 if j[0] == uniqueHD[l]:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	510 count[l, 0] = j[1]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	511 if state == 2:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	512 for k, l in zip(uniqueHD, nr):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	513 for j in table:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	514 if j[0] == uniqueHD[l]:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	515 count[l, 1] = j[1]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	516 if state == 3:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	517 for k, l in zip(uniqueHD, nr):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	518 for j in table:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	519 if j[0] == uniqueHD[l]:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	520 count[l, 2] = j[1]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	521 state = state + 1
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	522 sumRow = count.sum(axis=1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	523 sumCol = count.sum(axis=0)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	524 first = ["TD={}".format(i) for i in uniqueHD]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	525 final = numpy.column_stack((first, count, sumRow))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	526 return (final, sumCol)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	527
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	528
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	529 def createFileHD(summary, sumCol, overallSum, output_file, name, sep):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	530 output_file.write(name)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	531 output_file.write("\n")
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	532 output_file.write("{}FS=1{}FS=2{}FS=3{}FS=4{}FS=5-10{}FS>10{}sum{}\n".format(
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	533 sep, sep, sep, sep, sep, sep, sep, sep))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	534 for item in summary:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	535 for nr in item:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	536 if "TD" not in nr and "diff" not in nr:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	537 nr = nr.astype(float)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	538 nr = nr.astype(int)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	539 output_file.write("{}{}".format(nr, sep))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	540 output_file.write("\n")
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	541 output_file.write("sum{}".format(sep))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	542 sumCol = map(int, sumCol)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	543 for el in sumCol:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	544 output_file.write("{}{}".format(el, sep))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	545 output_file.write("{}{}".format(overallSum.astype(int), sep))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	546 output_file.write("\n\n")
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	547
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	548
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	549 def createFileHDwithDCS(summary, sumCol, overallSum, output_file, name, sep):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	550 output_file.write(name)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	551 output_file.write("\n")
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	552 output_file.write("{}DCS{}SSCS ab{}SSCS ba{}sum{}\n".format(sep, sep, sep, sep, sep))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	553 for item in summary:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	554 for nr in item:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	555 if "TD" not in nr:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	556 nr = nr.astype(float)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	557 nr = nr.astype(int)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	558 output_file.write("{}{}".format(nr, sep))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	559 output_file.write("\n")
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	560 output_file.write("sum{}".format(sep))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	561 sumCol = map(int, sumCol)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	562 for el in sumCol:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	563 output_file.write("{}{}".format(el, sep))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	564 output_file.write("{}{}".format(overallSum.astype(int), sep))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	565 output_file.write("\n\n")
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	566
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	567
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	568 def createFileHDwithinTag(summary, sumCol, overallSum, output_file, name, sep):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	569 output_file.write(name)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	570 output_file.write("\n")
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	571 output_file.write("{}TD a.min{}TD b.max{}TD b.min{}TD a.max{}TD a.min + b.max, TD a.max + b.min{}sum{}\n".format(sep, sep, sep, sep, sep, sep, sep))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	572 for item in summary:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	573 for nr in item:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	574 if "TD" not in nr:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	575 nr = nr.astype(float)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	576 nr = nr.astype(int)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	577 output_file.write("{}{}".format(nr, sep))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	578 output_file.write("\n")
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	579 output_file.write("sum{}".format(sep))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	580 sumCol = map(int, sumCol)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	581 for el in sumCol:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	582 output_file.write("{}{}".format(el, sep))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	583 output_file.write("{}{}".format(overallSum.astype(int), sep))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	584 output_file.write("\n\n")
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	585
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	586
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	587 def hamming(array1, array2):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	588 res = 99 * numpy.ones(len(array1))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	589 i = 0
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	590 array2 = numpy.unique(array2) # remove duplicate sequences to decrease running time
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	591 for a in array1:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	592 dist = numpy.array([sum(itertools.imap(operator.ne, a, b)) for b in array2]) # fastest
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	593 res[i] = numpy.amin(dist[dist > 0]) # pick min distance greater than zero
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	594 i += 1
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	595 return res
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	596
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	597
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	598 def hamming_difference(array1, array2, mate_b):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	599 array2 = numpy.unique(array2) # remove duplicate sequences to decrease running time
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	600 array1_half = numpy.array([i[0:(len(i)) / 2] for i in array1]) # mate1 part1
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	601 array1_half2 = numpy.array([i[len(i) / 2:len(i)] for i in array1]) # mate1 part 2
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	602 array2_half = numpy.array([i[0:(len(i)) / 2] for i in array2]) # mate2 part1
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	603 array2_half2 = numpy.array([i[len(i) / 2:len(i)] for i in array2]) # mate2 part2
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	604
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	605 # diff11 = 999 * numpy.ones(len(array2))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	606 # relativeDiffList = 999 * numpy.ones(len(array2))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	607 # ham1 = 999 * numpy.ones(len(array2))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	608 # ham2 = 999 * numpy.ones(len(array2))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	609 # min_valueList = 999 * numpy.ones(len(array2))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	610 # min_tagsList = 999 * numpy.ones(len(array2))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	611 # diff11_zeros = 999 * numpy.ones(len(array2))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	612 # min_tagsList_zeros = 999 * numpy.ones(len(array2))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	613
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	614 diff11 = []
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	615 relativeDiffList = []
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	616 ham1 = []
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	617 ham2 = []
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	618 ham1min = []
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	619 ham2min = []
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	620 min_valueList = []
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	621 min_tagsList = []
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	622 diff11_zeros = []
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	623 min_tagsList_zeros = []
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	624 max_tag_list = []
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	625 i = 0 # counter, only used to see how many HDs of tags were already calculated
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	626 if mate_b is False: # HD calculation for all a's
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	627 half1_mate1 = array1_half
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	628 half2_mate1 = array1_half2
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	629 half1_mate2 = array2_half
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	630 half2_mate2 = array2_half2
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	631 elif mate_b is True: # HD calculation for all b's
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	632 half1_mate1 = array1_half2
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	633 half2_mate1 = array1_half
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	634 half1_mate2 = array2_half2
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	635 half2_mate2 = array2_half
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	636
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	637 # half1_mate1, index_halves = numpy.unique(half1_mate1, return_index=True)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	638 # print(len(half1_mate1))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	639 # half2_mate1 = half2_mate1[index_halves]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	640 # array1 = array1[index_halves]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	641
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	642 for a, b, tag in zip(half1_mate1, half2_mate1, array1):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	643 # exclude identical tag from array2, to prevent comparison to itself
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	644 sameTag = numpy.where(array2 == tag)[0]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	645 indexArray2 = numpy.arange(0, len(array2), 1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	646 index_withoutSame = numpy.delete(indexArray2, sameTag) # delete identical tag from the data
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	647
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	648 # all tags without identical tag
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	649 array2_half_withoutSame = half1_mate2[index_withoutSame]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	650 array2_half2_withoutSame = half2_mate2[index_withoutSame]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	651 array2_withoutSame = array2[index_withoutSame] # whole tag (=not splitted into 2 halfs)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	652 # calculate HD of "a" in the tag to all "a's" or "b" in the tag to all "b's"
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	653 dist = numpy.array([sum(itertools.imap(operator.ne, a, c)) for c in
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	654 array2_half_withoutSame])
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	655 min_index = numpy.where(dist == dist.min())[0] # get index of min HD
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	656 min_value = dist.min()
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	657 # min_value = dist[min_index] # get minimum HDs
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	658 # get all "b's" of the tag or all "a's" of the tag with minimum HD
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	659 min_tag_half2 = array2_half2_withoutSame[min_index]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	660 min_tag_array2 = array2_withoutSame[min_index] # get whole tag with min HD
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	661
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	662 dist_second_half = numpy.array([sum(itertools.imap(operator.ne, b, e)) for e in
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	663 min_tag_half2]) # calculate HD of "b" to all "b's" or "a" to all "a's"
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	664 max_value = dist_second_half.max()
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	665 max_index = numpy.where(dist_second_half == dist_second_half.max())[0] # get index of max HD
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	666 max_tag = min_tag_array2[max_index]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	667
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	668 # for d, d2 in zip(min_value, max_value):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	669 if mate_b is True: # half2, corrects the variable of the HD from both halfs if it is a or b
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	670 ham2.append(min_value)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	671 ham2min.append(max_value)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	672 else: # half1, corrects the variable of the HD from both halfs if it is a or b
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	673 ham1.append(min_value)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	674 ham1min.append(max_value)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	675
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	676 min_valueList.append(min_value + max_value)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	677 min_tagsList.append(tag)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	678 difference1 = abs(min_value - max_value)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	679 diff11.append(difference1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	680 rel_difference = round(float(difference1) / (min_value + max_value), 1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	681 relativeDiffList.append(rel_difference)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	682
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	683 # tags which have identical parts:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	684 if min_value == 0 or max_value == 0:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	685 min_tagsList_zeros.append(numpy.array(tag))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	686 difference1_zeros = abs(min_value - max_value) # td of non-identical part
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	687 diff11_zeros.append(difference1_zeros)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	688 max_tag_list.append(numpy.array(max_tag))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	689 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	690 min_tagsList_zeros.append(None)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	691 diff11_zeros.append(None)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	692 max_tag_list.append(None)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	693 i += 1
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	694
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	695 # print(i)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	696 # diff11 = [st for st in diff11 if st != 999]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	697 # ham1 = [st for st in ham1 if st != 999]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	698 # ham2 = [st for st in ham2 if st != 999]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	699 # min_valueList = [st for st in min_valueList if st != 999]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	700 # min_tagsList = [st for st in min_tagsList if st != 999]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	701 # relativeDiffList = [st for st in relativeDiffList if st != 999]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	702 # diff11_zeros = [st for st in diff11_zeros if st != 999]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	703 # min_tagsList_zeros = [st for st in min_tagsList_zeros if st != 999]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	704 return ([diff11, ham1, ham2, min_valueList, min_tagsList, relativeDiffList, diff11_zeros,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	705 min_tagsList_zeros, ham1min, ham2min, max_tag_list])
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	706
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	707
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	708 def readFileReferenceFree(file):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	709 with open(file, 'r') as dest_f:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	710 data_array = numpy.genfromtxt(dest_f, skip_header=0, delimiter='\t', comments='#', dtype='string')
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	711 integers = numpy.array(data_array[:, 0]).astype(int)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	712 return(integers, data_array)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	713
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	714
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	715 def hammingDistanceWithFS(fs, ham):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	716 fs = numpy.asarray(fs)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	717 maximum = max(ham)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	718 minimum = min(ham)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	719 ham = numpy.asarray(ham)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	720
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	721 singletons = numpy.where(fs == 1)[0]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	722 data = ham[singletons]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	723
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	724 hd2 = numpy.where(fs == 2)[0]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	725 data2 = ham[hd2]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	726
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	727 hd3 = numpy.where(fs == 3)[0]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	728 data3 = ham[hd3]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	729
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	730 hd4 = numpy.where(fs == 4)[0]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	731 data4 = ham[hd4]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	732
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	733 hd5 = numpy.where((fs >= 5) & (fs <= 10))[0]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	734 data5 = ham[hd5]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	735
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	736 hd6 = numpy.where(fs > 10)[0]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	737 data6 = ham[hd6]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	738
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	739 list1 = [data, data2, data3, data4, data5, data6]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	740 return(list1, maximum, minimum)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	741
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	742
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	743 def familySizeDistributionWithHD(fs, ham, diff=False, rel=True):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	744 hammingDistances = numpy.unique(ham)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	745 fs = numpy.asarray(fs)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	746 ham = numpy.asarray(ham)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	747 bigFamilies2 = numpy.where(fs > 19)[0]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	748 if len(bigFamilies2) != 0:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	749 fs[bigFamilies2] = 20
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	750 maximum = max(fs)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	751 minimum = min(fs)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	752 if diff is True:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	753 hd0 = numpy.where(ham == 0)[0]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	754 data0 = fs[hd0]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	755
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	756 if rel is True:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	757 hd1 = numpy.where(ham == 0.1)[0]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	758 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	759 hd1 = numpy.where(ham == 1)[0]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	760 data = fs[hd1]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	761
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	762 if rel is True:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	763 hd2 = numpy.where(ham == 0.2)[0]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	764 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	765 hd2 = numpy.where(ham == 2)[0]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	766 data2 = fs[hd2]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	767
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	768 if rel is True:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	769 hd3 = numpy.where(ham == 0.3)[0]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	770 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	771 hd3 = numpy.where(ham == 3)[0]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	772 data3 = fs[hd3]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	773
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	774 if rel is True:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	775 hd4 = numpy.where(ham == 0.4)[0]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	776 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	777 hd4 = numpy.where(ham == 4)[0]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	778 data4 = fs[hd4]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	779
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	780 if rel is True:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	781 hd5 = numpy.where((ham >= 0.5) & (ham <= 0.8))[0]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	782 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	783 hd5 = numpy.where((ham >= 5) & (ham <= 8))[0]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	784 data5 = fs[hd5]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	785
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	786 if rel is True:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	787 hd6 = numpy.where(ham > 0.8)[0]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	788 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	789 hd6 = numpy.where(ham > 8)[0]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	790 data6 = fs[hd6]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	791
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	792 if diff is True:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	793 list1 = [data0, data, data2, data3, data4, data5, data6]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	794 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	795 list1 = [data, data2, data3, data4, data5, data6]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	796
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	797 return(list1, hammingDistances, maximum, minimum)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	798
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	799
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	800 def hammingDistanceWithDCS(minHD_tags_zeros, diff_zeros, data_array):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	801 diff_zeros = numpy.array(diff_zeros)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	802 maximum = numpy.amax(diff_zeros)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	803 minimum = numpy.amin(diff_zeros)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	804 minHD_tags_zeros = numpy.array(minHD_tags_zeros)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	805
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	806 idx = numpy.concatenate([numpy.where(data_array[:, 1] == i)[0] for i in minHD_tags_zeros])
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	807 subset_data = data_array[idx, :]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	808
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	809 seq = numpy.array(subset_data[:, 1])
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	810
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	811 # find all unique tags and get the indices for ALL tags, but only once
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	812 u, index_unique, c = numpy.unique(numpy.array(seq), return_counts=True, return_index=True)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	813 DCS_tags = u[c == 2]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	814 rest_tags = u[c == 1]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	815
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	816 dcs = numpy.repeat("DCS", len(DCS_tags))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	817 idx_sscs = numpy.concatenate([numpy.where(subset_data[:, 1] == i)[0] for i in rest_tags])
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	818 sscs = subset_data[idx_sscs, 2]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	819
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	820 all_tags = numpy.column_stack((numpy.concatenate((DCS_tags, subset_data[idx_sscs, 1])),
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	821 numpy.concatenate((dcs, sscs))))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	822 hd_DCS = []
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	823 ab_SSCS = []
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	824 ba_SSCS = []
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	825
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	826 for i in range(len(all_tags)):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	827 tag = all_tags[i, :]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	828 hd = diff_zeros[numpy.where(minHD_tags_zeros == tag[0])[0]]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	829
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	830 if tag[1] == "DCS":
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	831 hd_DCS.append(hd)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	832 elif tag[1] == "ab":
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	833 ab_SSCS.append(hd)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	834 elif tag[1] == "ba":
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	835 ba_SSCS.append(hd)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	836
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	837 if len(hd_DCS) != 0:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	838 hd_DCS = numpy.concatenate(hd_DCS)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	839 if len(ab_SSCS) != 0:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	840 ab_SSCS = numpy.concatenate(ab_SSCS)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	841 if len(ba_SSCS) != 0:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	842 ba_SSCS = numpy.concatenate(ba_SSCS)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	843 list1 = [hd_DCS, ab_SSCS, ba_SSCS] # list for plotting
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	844 return(list1, maximum, minimum)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	845
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	846
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	847 def make_argparser():
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	848 parser = argparse.ArgumentParser(description='Tag distance analysis of duplex sequencing data')
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	849 parser.add_argument('--inputFile',
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	850 help='Tabular File with three columns: ab or ba, tag and family size.')
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	851 parser.add_argument('--inputName1')
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	852 parser.add_argument('--sample_size', default=1000, type=int,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	853 help='Sample size of Tag distance analysis.')
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	854 parser.add_argument('--subset_tag', default=0, type=int,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	855 help='The tag is shortened to the given number.')
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	856 parser.add_argument('--nproc', default=4, type=int,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	857 help='The tool runs with the given number of processors.')
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	858 parser.add_argument('--only_DCS', action="store_false",
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	859 help='Only tags of the DCSs are included in the HD analysis')
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	860
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	861 parser.add_argument('--minFS', default=1, type=int,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	862 help='Only tags, which have a family size greater or equal than specified, '
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	863 'are included in the HD analysis')
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	864 parser.add_argument('--maxFS', default=0, type=int,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	865 help='Only tags, which have a family size smaller or equal than specified, '
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	866 'are included in the HD analysis')
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	867 parser.add_argument('--nr_above_bars', action="store_true",
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	868 help='If False, values above bars in the histograms are removed')
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	869 parser.add_argument('--rel_freq', action="store_false",
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	870 help='If True, the relative frequencies are displayed.')
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	871
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	872 parser.add_argument('--output_tabular', default="data.tabular", type=str,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	873 help='Name of the tabular file.')
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	874 parser.add_argument('--output_pdf', default="data.pdf", type=str,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	875 help='Name of the pdf file.')
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	876 parser.add_argument('--output_chimeras_tabular', default="data.tabular", type=str,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	877 help='Name of the tabular file with all chimeric tags.')
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	878
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	879 return parser
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	880
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	881
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	882 def Hamming_Distance_Analysis(argv):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	883 parser = make_argparser()
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	884 args = parser.parse_args(argv[1:])
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	885 file1 = args.inputFile
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	886 name1 = args.inputName1
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	887 index_size = args.sample_size
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	888 title_savedFile_pdf = args.output_pdf
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	889 title_savedFile_csv = args.output_tabular
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	890 output_chimeras_tabular = args.output_chimeras_tabular
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	891 onlyDuplicates = args.only_DCS
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	892 rel_freq = args.rel_freq
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	893 minFS = args.minFS
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	894 maxFS = args.maxFS
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	895 nr_above_bars = args.nr_above_bars
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	896 subset = args.subset_tag
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	897 nproc = args.nproc
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	898 sep = "\t"
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	899
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	900 # input checks
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	901 if index_size < 0:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	902 print("index_size is a negative integer.")
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	903 exit(2)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	904 if nproc <= 0:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	905 print("nproc is smaller or equal zero")
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	906 exit(3)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	907 if subset < 0:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	908 print("subset_tag is smaller or equal zero.")
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	909 exit(5)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	910
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	911 # PLOT
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	912 plt.rcParams['axes.facecolor'] = "E0E0E0" # grey background color
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	913 plt.rcParams['xtick.labelsize'] = 14
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	914 plt.rcParams['ytick.labelsize'] = 14
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	915 plt.rcParams['patch.edgecolor'] = "#000000"
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	916 plt.rc('figure', figsize=(11.69, 8.27)) # A4 format
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	917 name1 = name1.split(".tabular")[0]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	918
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	919 with open(title_savedFile_csv, "w") as output_file, PdfPages(title_savedFile_pdf) as pdf:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	920 print("dataset: ", name1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	921 integers, data_array = readFileReferenceFree(file1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	922 data_array = numpy.array(data_array)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	923 print("total nr of tags:", len(data_array))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	924
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	925 # filter tags out which contain any other character than ATCG
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	926 valid_bases = ["A", "T", "G", "C"]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	927 tagsToDelete = []
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	928 for idx, t in enumerate(data_array[:, 1]):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	929 for char in t:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	930 if char not in valid_bases:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	931 tagsToDelete.append(idx)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	932 break
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	933
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	934 if len(tagsToDelete) != 0: # delete tags with N in the tag from data
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	935 print("nr of tags with any other character than A, T, C, G:", len(tagsToDelete),
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	936 float(len(tagsToDelete)) / len(data_array))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	937 index_whole_array = numpy.arange(0, len(data_array), 1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	938 index_withoutN_inTag = numpy.delete(index_whole_array, tagsToDelete)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	939 data_array = data_array[index_withoutN_inTag, :]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	940 integers = integers[index_withoutN_inTag]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	941 print("total nr of filtered tags:", len(data_array))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	942
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	943 int_f = numpy.array(data_array[:, 0]).astype(int)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	944 data_array = data_array[numpy.where(int_f >= minFS)]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	945 integers = integers[integers >= minFS]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	946
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	947 # select family size for tags
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	948 if maxFS > 0:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	949 int_f2 = numpy.array(data_array[:, 0]).astype(int)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	950 data_array = data_array[numpy.where(int_f2 <= maxFS)]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	951 integers = integers[integers <= maxFS]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	952
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	953 if onlyDuplicates is True:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	954 tags = data_array[:, 2]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	955 seq = data_array[:, 1]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	956
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	957 # find all unique tags and get the indices for ALL tags, but only once
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	958 u, index_unique, c = numpy.unique(numpy.array(seq), return_counts=True, return_index=True)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	959 d = u[c == 2]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	960
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	961 # get family sizes, tag for duplicates
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	962 duplTags_double = integers[numpy.in1d(seq, d)]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	963 duplTags = duplTags_double[0::2] # ab of DCS
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	964 duplTagsBA = duplTags_double[1::2] # ba of DCS
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	965
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	966 duplTags_tag = tags[numpy.in1d(seq, d)][0::2] # ab
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	967 duplTags_seq = seq[numpy.in1d(seq, d)][0::2] # ab - tags
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	968
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	969 if minFS > 1:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	970 duplTags_tag = duplTags_tag[(duplTags >= minFS) & (duplTagsBA >= minFS)]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	971 duplTags_seq = duplTags_seq[(duplTags >= minFS) & (duplTagsBA >= minFS)]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	972 duplTags = duplTags[(duplTags >= minFS) & (duplTagsBA >= minFS)] # ab+ba with FS>=3
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	973
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	974 data_array = numpy.column_stack((duplTags, duplTags_seq))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	975 data_array = numpy.column_stack((data_array, duplTags_tag))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	976 integers = numpy.array(data_array[:, 0]).astype(int)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	977 print("DCS in whole dataset", len(data_array))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	978
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	979 print("min FS", min(integers))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	980 print("max FS", max(integers))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	981
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	982 # HD analysis for a subset of the tag
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	983 if subset > 0:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	984 tag1 = numpy.array([i[0:(len(i)) / 2] for i in data_array[:, 1]])
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	985 tag2 = numpy.array([i[len(i) / 2:len(i)] for i in data_array[:, 1]])
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	986
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	987 flanking_region_float = float((len(tag1[0]) - subset)) / 2
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	988 flanking_region = int(flanking_region_float)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	989 if flanking_region_float % 2 == 0:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	990 tag1_shorten = numpy.array([i[flanking_region:len(i) - flanking_region] for i in tag1])
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	991 tag2_shorten = numpy.array([i[flanking_region:len(i) - flanking_region] for i in tag2])
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	992 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	993 flanking_region_rounded = int(round(flanking_region, 1))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	994 flanking_region_rounded_end = len(tag1[0]) - subset - flanking_region_rounded
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	995 tag1_shorten = numpy.array(
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	996 [i[flanking_region:len(i) - flanking_region_rounded_end] for i in tag1])
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	997 tag2_shorten = numpy.array(
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	998 [i[flanking_region:len(i) - flanking_region_rounded_end] for i in tag2])
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	999
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1000 data_array_tag = numpy.array([i + j for i, j in zip(tag1_shorten, tag2_shorten)])
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1001 data_array = numpy.column_stack((data_array[:, 0], data_array_tag, data_array[:, 2]))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1002
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1003 print("length of tag= ", len(data_array[0, 1]))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1004 # select sample: if no size given --> all vs. all comparison
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1005 if index_size == 0:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1006 result = numpy.arange(0, len(data_array), 1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1007 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1008 numpy.random.shuffle(data_array)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1009 unique_tags, unique_indices = numpy.unique(data_array[:, 1], return_index=True) # get only unique tags
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1010 result = numpy.random.choice(unique_indices, size=index_size,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1011 replace=False) # array of random sequences of size=index.size
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1012
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1013 # result = numpy.random.choice(len(integers), size=index_size,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1014 # replace=False) # array of random sequences of size=index.size
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1015 # result = numpy.where(numpy.array(random_tags) == numpy.array(data_array[:,1]))[0]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1016
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1017 # with open("index_result.pkl", "wb") as o:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1018 # pickle.dump(result, o, pickle.HIGHEST_PROTOCOL)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1019
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1020 # save counts
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1021 # with open(data_folder + "index_sampleTags1000_Barcode3_DCS.pkl", "wb") as f:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1022 # pickle.dump(result, f, pickle.HIGHEST_PROTOCOL)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1023 # with open(data_folder + "dataArray_sampleTags1000_Barcode3_DCS.pkl", "wb") as f1:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1024 # pickle.dump(data_array, f1, pickle.HIGHEST_PROTOCOL)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1025 #
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1026 # with open(data_folder + "index_sampleTags100.pkl", "rb") as f:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1027 # result = pickle.load(f)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1028 #
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1029 # with open(data_folder + "dataArray_sampleTags100.pkl", "rb") as f1:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1030 # data_array = pickle.load(f1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1031
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1032 # with open(data_folder + "index_result.txt", "w") as t:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1033 # for text in result:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1034 # t.write("{}\n".format(text))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1035
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1036 # comparison random tags to whole dataset
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1037 result1 = data_array[result, 1] # random tags
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1038 result2 = data_array[:, 1] # all tags
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1039 print("sample size= ", len(result1))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1040
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1041 # HD analysis of whole tag
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1042 proc_pool = Pool(nproc)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1043 chunks_sample = numpy.array_split(result1, nproc)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1044 ham = proc_pool.map(partial(hamming, array2=result2), chunks_sample)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1045 proc_pool.close()
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1046 proc_pool.join()
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1047 ham = numpy.concatenate(ham).astype(int)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1048 # with open("HD_whole dataset_{}.txt".format(app_f), "w") as output_file1:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1049 # for h, tag in zip(ham, result1):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1050 # output_file1.write("{}\t{}\n".format(tag, h))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1051
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1052 # # HD analysis for chimeric reads
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1053 # result2 = data_array_whole_dataset[:,1]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1054
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1055 proc_pool_b = Pool(nproc)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1056 diff_list_a = proc_pool_b.map(partial(hamming_difference, array2=result2, mate_b=False), chunks_sample)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1057 diff_list_b = proc_pool_b.map(partial(hamming_difference, array2=result2, mate_b=True), chunks_sample)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1058 proc_pool_b.close()
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1059 proc_pool_b.join()
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1060 HDhalf1 = numpy.concatenate((numpy.concatenate([item[1] for item in diff_list_a]),
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1061 numpy.concatenate([item_b[1] for item_b in diff_list_b]))).astype(int)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1062 HDhalf2 = numpy.concatenate((numpy.concatenate([item[2] for item in diff_list_a]),
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1063 numpy.concatenate([item_b[2] for item_b in diff_list_b]))).astype(int)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1064 minHDs = numpy.concatenate((numpy.concatenate([item[3] for item in diff_list_a]),
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1065 numpy.concatenate([item_b[3] for item_b in diff_list_b]))).astype(int)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1066 HDhalf1min = numpy.concatenate((numpy.concatenate([item[8] for item in diff_list_a]),
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1067 numpy.concatenate([item_b[8] for item_b in diff_list_b]))).astype(int)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1068 HDhalf2min = numpy.concatenate((numpy.concatenate([item[9] for item in diff_list_a]),
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1069 numpy.concatenate([item_b[9] for item_b in diff_list_b]))).astype(int)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1070
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1071 rel_Diff1 = numpy.concatenate([item[5] for item in diff_list_a])
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1072 rel_Diff2 = numpy.concatenate([item[5] for item in diff_list_b])
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1073 diff1 = numpy.concatenate([item[0] for item in diff_list_a])
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1074 diff2 = numpy.concatenate([item[0] for item in diff_list_b])
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1075
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1076 diff_zeros1 = numpy.concatenate([item[6] for item in diff_list_a])
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1077 diff_zeros2 = numpy.concatenate([item[6] for item in diff_list_b])
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1078 minHD_tags = numpy.concatenate([item[4] for item in diff_list_a])
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1079 minHD_tags_zeros1 = numpy.concatenate([item[7] for item in diff_list_a])
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1080 minHD_tags_zeros2 = numpy.concatenate([item[7] for item in diff_list_b])
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1081
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1082 chimera_tags1 = sum([item[10] for item in diff_list_a], [])
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1083 chimera_tags2 = sum([item[10] for item in diff_list_b], [])
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1084
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1085 rel_Diff = []
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1086 diff_zeros = []
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1087 minHD_tags_zeros = []
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1088 diff = []
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1089 chimera_tags = []
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1090 for d1, d2, rel1, rel2, zeros1, zeros2, tag1, tag2, ctag1, ctag2 in \
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1091 zip(diff1, diff2, rel_Diff1, rel_Diff2, diff_zeros1, diff_zeros2, minHD_tags_zeros1, minHD_tags_zeros2,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1092 chimera_tags1, chimera_tags2):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1093 relatives = numpy.array([rel1, rel2])
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1094 absolutes = numpy.array([d1, d2])
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1095 max_idx = numpy.argmax(relatives)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1096 rel_Diff.append(relatives[max_idx])
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1097 diff.append(absolutes[max_idx])
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1098
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1099 if all(i is not None for i in [zeros1, zeros2]):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1100 diff_zeros.append(max(zeros1, zeros2))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1101 minHD_tags_zeros.append(str(tag1))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1102 tags = [ctag1, ctag2]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1103 chimera_tags.append(tags)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1104 elif zeros1 is not None and zeros2 is None:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1105 diff_zeros.append(zeros1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1106 minHD_tags_zeros.append(str(tag1))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1107 chimera_tags.append(ctag1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1108 elif zeros1 is None and zeros2 is not None:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1109 diff_zeros.append(zeros2)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1110 minHD_tags_zeros.append(str(tag2))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1111 chimera_tags.append(ctag2)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1112
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1113 chimera_tags_new = chimera_tags
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1114 data_chimeraAnalysis = numpy.column_stack((minHD_tags_zeros, chimera_tags_new))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1115 # chimeras_dic = defaultdict(list)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1116 #
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1117 # for t1, t2 in zip(minHD_tags_zeros, chimera_tags_new):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1118 # if len(t2) >1 and type(t2) is not numpy.ndarray:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1119 # t2 = numpy.concatenate(t2)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1120 # chimeras_dic[t1].append(t2)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1121
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1122 checked_tags = []
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1123 stat_maxTags = []
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1124
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1125 with open(output_chimeras_tabular, "w") as output_file1:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1126 output_file1.write("chimera tag\tfamily size, read direction\tsimilar tag with TD=0\n")
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1127 for i in range(len(data_chimeraAnalysis)):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1128 tag1 = data_chimeraAnalysis[i, 0]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1129
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1130 info_tag1 = data_array[data_array[:, 1] == tag1, :]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1131 fs_tag1 = ["{} {}".format(t[0], t[2]) for t in info_tag1]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1132
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1133 if tag1 in checked_tags: # skip tag if already written to file
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1134 continue
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1135
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1136 sample_half_a = tag1[0:(len(tag1)) / 2]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1137 sample_half_b = tag1[len(tag1) / 2:len(tag1)]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1138
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1139 max_tags = data_chimeraAnalysis[i, 1]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1140 if len(max_tags) > 1 and len(max_tags) != len(data_array[0, 1]) and type(max_tags) is not numpy.ndarray:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1141 max_tags = numpy.concatenate(max_tags)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1142 max_tags = numpy.unique(max_tags)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1143 stat_maxTags.append(len(max_tags))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1144
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1145 info_maxTags = [data_array[data_array[:, 1] == t, :] for t in max_tags]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1146
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1147 chimera_half_a = numpy.array([t[0:(len(t)) / 2] for t in max_tags]) # mate1 part1
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1148 chimera_half_b = numpy.array([t[len(t) / 2:len(t)] for t in max_tags]) # mate1 part 2
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1149
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1150 new_format = []
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1151 for j in range(len(max_tags)):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1152 fs_maxTags = ["{} {}".format(t[0], t[2]) for t in info_maxTags[j]]
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1153
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1154 if sample_half_a == chimera_half_a[j]:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1155 max_tag = "{} {} {}".format(chimera_half_a[j], chimera_half_b[j], ", ".join(fs_maxTags))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1156 new_format.append(max_tag)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1157
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1158 elif sample_half_b == chimera_half_b[j]:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1159 max_tag = "{} {} {}".format(chimera_half_a[j], chimera_half_b[j], ", ".join(fs_maxTags))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1160 new_format.append(max_tag)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1161 checked_tags.append(max_tags[j])
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1162
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1163 sample_tag = "{} {}\t{}".format(sample_half_a, sample_half_b, ", ".join(fs_tag1))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1164 output_file1.write("{}\t{}\n".format(sample_tag, ", ".join(new_format)))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1165
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1166 checked_tags.append(tag1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1167
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1168 output_file1.write(
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1169 "This file contains all tags that were identified as chimeras as the first column and the "
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1170 "corresponding tags which returned a Hamming distance of zero in either the first or the second "
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1171 "half of the sample tag as the second column.\n"
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1172 "The tags were separated by an empty space into their halves and the * marks the identical half.")
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1173 output_file1.write("\n\nStatistics of nr. of tags that returned max. TD (2nd column)\n")
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1174 output_file1.write("minimum\t{}\ttag(s)\n".format(numpy.amin(numpy.array(stat_maxTags))))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1175 output_file1.write("mean\t{}\ttag(s)\n".format(numpy.mean(numpy.array(stat_maxTags))))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1176 output_file1.write("median\t{}\ttag(s)\n".format(numpy.median(numpy.array(stat_maxTags))))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1177 output_file1.write("maximum\t{}\ttag(s)\n".format(numpy.amax(numpy.array(stat_maxTags))))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1178 output_file1.write("sum\t{}\ttag(s)\n".format(numpy.sum(numpy.array(stat_maxTags))))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1179
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1180 lenTags = len(data_array)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1181 len_sample = len(result1)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1182
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1183 quant = numpy.array(data_array[result, 0]).astype(int) # family size for sample of tags
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1184 seq = numpy.array(data_array[result, 1]) # tags of sample
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1185 ham = numpy.asarray(ham) # HD for sample of tags
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1186
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1187 if onlyDuplicates is True: # ab and ba strands of DCSs
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1188 quant = numpy.concatenate((quant, duplTagsBA[result]))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1189 seq = numpy.tile(seq, 2)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1190 ham = numpy.tile(ham, 2)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1191 diff = numpy.tile(diff, 2)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1192 rel_Diff = numpy.tile(rel_Diff, 2)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1193 diff_zeros = numpy.tile(diff_zeros, 2)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1194
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1195 nr_chimeric_tags = len(data_chimeraAnalysis)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1196 print("nr of chimeras", nr_chimeric_tags)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1197
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1198 # prepare data for different kinds of plots
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1199 # distribution of FSs separated after HD
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1200 familySizeList1, hammingDistances, maximumXFS, minimumXFS = familySizeDistributionWithHD(quant, ham, rel=False)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1201 list1, maximumX, minimumX = hammingDistanceWithFS(quant, ham) # histogram of HDs separated after FS
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1202
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1203 # get FS for all tags with min HD of analysis of chimeric reads
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1204 # there are more tags than sample size in the plot, because one tag can have multiple minimas
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1205 if onlyDuplicates:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1206 seqDic = defaultdict(list)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1207 for s, q in zip(seq, quant):
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1208 seqDic[s].append(q)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1209 else:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1210 seqDic = dict(zip(seq, quant))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1211
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1212 lst_minHD_tags = []
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1213 for i in minHD_tags:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1214 lst_minHD_tags.append(seqDic.get(i))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1215
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1216 if onlyDuplicates:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1217 lst_minHD_tags = numpy.concatenate(([item[0] for item in lst_minHD_tags],
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1218 [item_b[1] for item_b in lst_minHD_tags])).astype(int)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1219 # histogram with absolute and relative difference between HDs of both parts of the tag
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1220 listDifference1, maximumXDifference, minimumXDifference = hammingDistanceWithFS(lst_minHD_tags, diff)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1221 listRelDifference1, maximumXRelDifference, minimumXRelDifference = hammingDistanceWithFS(lst_minHD_tags,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1222 rel_Diff)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1223 # chimeric read analysis: tags which have TD=0 in one of the halfs
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1224 if len(minHD_tags_zeros) != 0:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1225 lst_minHD_tags_zeros = []
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1226 for i in minHD_tags_zeros:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1227 lst_minHD_tags_zeros.append(seqDic.get(i)) # get family size for tags of chimeric reads
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1228 if onlyDuplicates:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1229 lst_minHD_tags_zeros = numpy.concatenate(([item[0] for item in lst_minHD_tags_zeros],
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1230 [item_b[1] for item_b in lst_minHD_tags_zeros])).astype(int)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1231
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1232 # histogram with HD of non-identical half
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1233 listDifference1_zeros, maximumXDifference_zeros, minimumXDifference_zeros = hammingDistanceWithFS(
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1234 lst_minHD_tags_zeros, diff_zeros)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1235
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1236 if onlyDuplicates is False:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1237 listDCS_zeros, maximumXDCS_zeros, minimumXDCS_zeros = hammingDistanceWithDCS(minHD_tags_zeros,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1238 diff_zeros, data_array)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1239
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1240 # plot Hamming Distance with Family size distribution
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1241 plotHDwithFSD(list1=list1, maximumX=maximumX, minimumX=minimumX, pdf=pdf, rel_freq=rel_freq,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1242 subtitle="Tag distance separated by family size", lenTags=lenTags,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1243 xlabel="TD", nr_above_bars=nr_above_bars, len_sample=len_sample)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1244
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1245 # Plot FSD with separation after
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1246 plotFSDwithHD2(familySizeList1, maximumXFS, minimumXFS, rel_freq=rel_freq,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1247 originalCounts=quant, subtitle="Family size distribution separated by Tag distance",
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1248 pdf=pdf, relative=False, diff=False)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1249
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1250 # Plot HD within tags
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1251 plotHDwithinSeq(HDhalf1, HDhalf1min, HDhalf2, HDhalf2min, minHDs, pdf=pdf, lenTags=lenTags,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1252 rel_freq=rel_freq, len_sample=len_sample)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1253
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1254 # Plot difference between HD's separated after FSD
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1255 plotHDwithFSD(listDifference1, maximumXDifference, minimumXDifference, pdf=pdf,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1256 subtitle="Delta Tag distance within tags", lenTags=lenTags, rel_freq=rel_freq,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1257 xlabel="absolute delta TD", relative=False, nr_above_bars=nr_above_bars, len_sample=len_sample)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1258
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1259 plotHDwithFSD(listRelDifference1, maximumXRelDifference, minimumXRelDifference, pdf=pdf,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1260 subtitle="Chimera Analysis: relative delta Tag distance", lenTags=lenTags, rel_freq=rel_freq,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1261 xlabel="relative delta TD", relative=True, nr_above_bars=nr_above_bars,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1262 nr_unique_chimeras=nr_chimeric_tags, len_sample=len_sample)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1263
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1264 # plots for chimeric reads
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1265 if len(minHD_tags_zeros) != 0:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1266 # HD
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1267 plotHDwithFSD(listDifference1_zeros, maximumXDifference_zeros, minimumXDifference_zeros, pdf=pdf,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1268 subtitle="Tag distance of chimeric families (CF)", rel_freq=rel_freq,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1269 lenTags=lenTags, xlabel="TD", relative=False,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1270 nr_above_bars=nr_above_bars, nr_unique_chimeras=nr_chimeric_tags, len_sample=len_sample)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1271
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1272 if onlyDuplicates is False:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1273 plotHDwithDCS(listDCS_zeros, maximumXDCS_zeros, minimumXDCS_zeros, pdf=pdf,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1274 subtitle="Tag distance of chimeric families (CF)", rel_freq=rel_freq,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1275 lenTags=lenTags, xlabel="TD", relative=False,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1276 nr_above_bars=nr_above_bars, nr_unique_chimeras=nr_chimeric_tags, len_sample=len_sample)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1277
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1278 # print all data to a CSV file
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1279 # HD
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1280 summary, sumCol = createTableHD(list1, "TD=")
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1281 overallSum = sum(sumCol) # sum of columns in table
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1282
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1283 # FSD
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1284 summary5, sumCol5 = createTableFSD2(familySizeList1, diff=False)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1285 overallSum5 = sum(sumCol5)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1286
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1287 # HD of both parts of the tag
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1288 summary9, sumCol9 = createTableHDwithTags([HDhalf1, HDhalf1min, HDhalf2, HDhalf2min, numpy.array(minHDs)])
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1289 overallSum9 = sum(sumCol9)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1290
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1291 # HD
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1292 # absolute difference
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1293 summary11, sumCol11 = createTableHD(listDifference1, "diff=")
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1294 overallSum11 = sum(sumCol11)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1295 # relative difference and all tags
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1296 summary13, sumCol13 = createTableHD(listRelDifference1, "diff=")
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1297 overallSum13 = sum(sumCol13)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1298
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1299 # chimeric reads
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1300 if len(minHD_tags_zeros) != 0:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1301 # absolute difference and tags where at least one half has HD=0
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1302 summary15, sumCol15 = createTableHD(listDifference1_zeros, "TD=")
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1303 overallSum15 = sum(sumCol15)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1304
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1305 if onlyDuplicates is False:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1306 summary16, sumCol16 = createTableHDwithDCS(listDCS_zeros)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1307 overallSum16 = sum(sumCol16)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1308
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1309 output_file.write("{}\n".format(name1))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1310 output_file.write("nr of tags{}{:,}\nsample size{}{:,}\n\n".format(sep, lenTags, sep, len_sample))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1311
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1312 # HD
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1313 createFileHD(summary, sumCol, overallSum, output_file,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1314 "Tag distance separated by family size", sep)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1315 # FSD
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1316 createFileFSD2(summary5, sumCol5, overallSum5, output_file,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1317 "Family size distribution separated by Tag distance", sep,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1318 diff=False)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1319
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1320 # output_file.write("{}{}\n".format(sep, name1))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1321 output_file.write("\n")
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1322 max_fs = numpy.bincount(integers[result])
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1323 output_file.write("max. family size in sample:{}{}\n".format(sep, max(integers[result])))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1324 output_file.write("absolute frequency:{}{}\n".format(sep, max_fs[len(max_fs) - 1]))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1325 output_file.write(
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1326 "relative frequency:{}{}\n\n".format(sep, float(max_fs[len(max_fs) - 1]) / sum(max_fs)))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1327
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1328 # HD within tags
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1329 output_file.write(
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1330 "Chimera Analysis:\nThe tags are splitted into two halves (part a and b) for which the Tag distances (TD) are calculated seperately.\n"
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1331 "The tag distance of the first half (part a) is calculated by comparing part a of the tag in the sample against all a parts in the dataset and by selecting the minimum value (TD a.min).\n"
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1332 "In the next step, we select those tags that showed the minimum TD and estimate the TD for the second half (part b) of the tag by comparing part b against the previously selected subset.\n"
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1333 "The maximum value represents then TD b.max. Finally, these process is repeated but starting with part b instead and TD b.min and TD a.max are calculated.\n"
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1334 "Next, the absolute differences between TD a.min & TD b.max and TD b.min & TD a.max are estimated (delta HD).\n"
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1335 "These are then divided by the sum of both parts (TD a.min + TD b.max or TD b.min + TD a.max, respectively) which give the relative differences between the partial HDs (rel. delta HD).\n"
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1336 "For simplicity, we used the maximum value of the relative differences and the respective delta HD.\n"
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1337 "Note that when only tags that can form a DCS are included in the analysis, the family sizes for both directions (ab and ba) of the strand will be included in the plots.\n")
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1338
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1339 output_file.write("\nlength of one half of the tag{}{}\n\n".format(sep, len(data_array[0, 1]) / 2))
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1340
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1341 createFileHDwithinTag(summary9, sumCol9, overallSum9, output_file,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1342 "Tag distance of each half in the tag", sep)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1343 createFileHD(summary11, sumCol11, overallSum11, output_file,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1344 "Absolute delta Tag distance within the tag", sep)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1345
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1346 createFileHD(summary13, sumCol13, overallSum13, output_file,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1347 "Chimera analysis: relative delta Tag distance", sep)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1348
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1349 if len(minHD_tags_zeros) != 0:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1350 output_file.write(
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1351 "All tags are filtered and only those tags where one half is identical (TD=0) and therefore, have a relative delta TD of 1, are kept.\n"
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1352 "These tags are considered as chimeras.\n")
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1353 createFileHD(summary15, sumCol15, overallSum15, output_file,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1354 "Tag distance of chimeric families separated after FS", sep)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1355
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1356 if onlyDuplicates is False:
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1357 createFileHDwithDCS(summary16, sumCol16, overallSum16, output_file,
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1358 "Tag distance of chimeric families separated after DCS and single SSCS (ab, ba)", sep)
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1359
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1360 output_file.write("\n")
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1361
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1362
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1363 if __name__ == '__main__':
3e56058d9552 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty mheinzl parents: diff changeset	1364 sys.exit(Hamming_Distance_Analysis(sys.argv))

Mercurial > repos > mheinzl > td

annotate td.py @ 0:3e56058d9552 draft default tip