hd: hd.py annotate

annotate hd.py @ 30:46bfbec0f9e6 draft

planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 033dd7b750f68e8aa68f327d7d72bd311ddbee4e-dirty

author	mheinzl
date	Wed, 07 Aug 2019 04:01:32 -0400
parents	6b15b3b6405c
children	8beced3064e3

rev	line source
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	1 #!/usr/bin/env python
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	2
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	3 # Hamming distance analysis of SSCSs
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	4 #
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	5 # Author: Monika Heinzl, Johannes-Kepler University Linz (Austria)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	6 # Contact: monika.heinzl@edumail.at
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	7 #
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	8 # Takes at least one TABULAR file with tags before the alignment to the SSCS and
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	9 # optionally a second TABULAR file as input. The program produces a plot which shows a histogram of Hamming distances
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	10 # separated after family sizes, a family size distribution separated after Hamming distances for all (sample_size=0)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 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
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 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
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	13 # data of the plots. It is also possible to perform the HD analysis with shortened tags with given sizes as input.
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	14 # The tool can run on a certain number of processors, which can be defined by the user.
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	15
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	16 # USAGE: python hd.py --inputFile filename --inputName1 filename --sample_size int /
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	17 # --only_DCS True --FamilySize3 True --subset_tag True --nproc int --minFS int --maxFS int
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	18 # --nr_above_bars True/False --output_tabular outptufile_name_tabular
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	19
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	20 import argparse
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	21 import itertools
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	22 import operator
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	23 import sys
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	24 from collections import Counter, defaultdict
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	25 from functools import partial
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	26 from multiprocessing.pool import Pool
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	27 import random
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	28 import os
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	29
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	30 import matplotlib.pyplot as plt
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	31 import numpy
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	32 from matplotlib.backends.backend_pdf import PdfPages
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	33
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	34 plt.switch_backend('agg')
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	35
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	36
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	37 def plotFSDwithHD2(familySizeList1, maximumXFS, minimumXFS, originalCounts,
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	38 subtitle, pdf, relative=False, diff=True, rel_freq=False):
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	39 if diff is False:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	40 colors = ["#e6194b", "#3cb44b", "#ffe119", "#0082c8", "#f58231", "#911eb4"]
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	41 labels = ["HD=1", "HD=2", "HD=3", "HD=4", "HD=5-8", "HD>8"]
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	42 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	43 colors = ["#93A6AB", "#403C14", "#731E41", "#BAB591", "#085B6F", "#E8AA35", "#726C66"]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	44 if relative is True:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 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"]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	46 else:
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	47 labels = ["d=0", "d=1", "d=2", "d=3", "d=4", "d=5-8", "d>8"]
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	48
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	49 fig = plt.figure(figsize=(6, 7))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	50 ax = fig.add_subplot(111)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	51 plt.subplots_adjust(bottom=0.1)
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	52 p1 = numpy.bincount(numpy.concatenate(familySizeList1))
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	53 maximumY = numpy.amax(p1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	54
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	55 if len(range(minimumXFS, maximumXFS)) == 0:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	56 range1 = range(minimumXFS - 1, minimumXFS + 2)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	57 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	58 range1 = range(0, maximumXFS + 2)
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	59
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	60 if rel_freq:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	61 w = [numpy.zeros_like(data) + 1. / len(numpy.concatenate(familySizeList1)) for data in familySizeList1]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	62 counts = plt.hist(familySizeList1, label=labels, weights=w, color=colors, stacked=True,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	63 rwidth=0.8, alpha=1, align="left", edgecolor="None", bins=range1)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	64 plt.ylabel("Relative Frequency", fontsize=14)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	65 plt.ylim((0, (float(maximumY) / sum(p1)) * 1.1))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	66 else:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	67 counts = plt.hist(familySizeList1, label=labels, color=colors, stacked=True,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	68 rwidth=0.8, alpha=1, align="left", edgecolor="None", bins=range1)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	69 if len(numpy.concatenate(familySizeList1)) != 0:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	70 plt.ylim((0, max(numpy.bincount(numpy.concatenate(familySizeList1))) * 1.1))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	71 plt.ylabel("Absolute Frequency", fontsize=14)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	72 plt.ylim((0, maximumY * 1.2))
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	73 plt.legend(loc='upper right', fontsize=14, frameon=True, bbox_to_anchor=(1.45, 1))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	74 plt.suptitle(subtitle, y=1, x=0.5, fontsize=14)
2 316fbf91dd12 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit f9d5547849dabb59a33a5e998bda4730323d62a9 mheinzl parents: 1 diff changeset	75 plt.xlabel("Family size", fontsize=14)
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	76 ticks = numpy.arange(0, maximumXFS + 1, 1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	77 ticks1 = map(str, ticks)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	78 if maximumXFS >= 20:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	79 ticks1[len(ticks1) - 1] = ">=20"
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	80 plt.xticks(numpy.array(ticks), ticks1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	81 [l.set_visible(False) for (i, l) in enumerate(ax.get_xticklabels()) if i % 5 != 0]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	82 plt.xlim((0, maximumXFS + 1))
21 9919024d7778 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6 mheinzl parents: 20 diff changeset	83 legend = "\nfamily size: \nabsolute frequency: \nrelative frequency: "
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	84 plt.text(0.15, -0.08, legend, size=12, transform=plt.gcf().transFigure)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	85
11 7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9 mheinzl parents: 10 diff changeset	86 count = numpy.bincount(originalCounts) # original counts
21 9919024d7778 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6 mheinzl parents: 20 diff changeset	87 if max(originalCounts) >= 20:
9919024d7778 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6 mheinzl parents: 20 diff changeset	88 max_count = ">= 20"
9919024d7778 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6 mheinzl parents: 20 diff changeset	89 else:
9919024d7778 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6 mheinzl parents: 20 diff changeset	90 max_count = max(originalCounts)
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	91 legend1 = "{}\n{}\n{:.5f}".format(max_count, p1[len(p1) - 1], float(p1[len(p1) - 1]) / sum(p1))
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	92 plt.text(0.5, -0.08, legend1, size=12, transform=plt.gcf().transFigure)
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	93 legend3 = "singletons\n{:,}\n{:.5f}".format(int(p1[1]), float(p1[1]) / sum(p1))
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	94 plt.text(0.7, -0.08, legend3, transform=plt.gcf().transFigure, size=12)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	95 plt.grid(b=True, which='major', color='#424242', linestyle=':')
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	96 pdf.savefig(fig, bbox_inches="tight")
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	97 plt.close("all")
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	98
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	99
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	100 def plotHDwithFSD(list1, maximumX, minimumX, subtitle, lenTags, pdf, xlabel, relative=False,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	101 nr_above_bars=True, nr_unique_chimeras=0, len_sample=0, rel_freq=False):
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	102 if relative is True:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	103 step = 0.1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	104 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	105 step = 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	106
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	107 fig = plt.figure(figsize=(6, 8))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	108 plt.subplots_adjust(bottom=0.1)
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	109 p1 = numpy.array([v for k, v in sorted(Counter(numpy.concatenate(list1)).iteritems())])
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	110 maximumY = numpy.amax(p1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	111 if relative is True: # relative difference
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	112 bin1 = numpy.arange(-1, maximumX + 0.2, 0.1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	113 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	114 bin1 = maximumX + 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	115
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	116 if rel_freq:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	117 w = [numpy.zeros_like(data) + 1. / len(numpy.concatenate(list1)) for data in list1]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	118 counts = plt.hist(list1, bins=bin1, edgecolor='black', linewidth=1, weights=w,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	119 label=["FS=1", "FS=2", "FS=3", "FS=4", "FS=5-10", "FS>10"], rwidth=0.8,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	120 color=["#808080", "#FFFFCC", "#FFBF00", "#DF0101", "#0431B4", "#86B404"],
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	121 stacked=True, alpha=1, align="left", range=(0, maximumX + 1))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	122 plt.ylim((0, (float(maximumY) / sum(p1)) * 1.2))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	123 plt.ylabel("Relative Frequency", fontsize=14)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	124 bins = counts[1] # width of bins
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	125 counts = numpy.array(map(float, counts[0][5]))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	126
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	127 else:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	128 counts = plt.hist(list1, bins=bin1, edgecolor='black', linewidth=1,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	129 label=["FS=1", "FS=2", "FS=3", "FS=4", "FS=5-10", "FS>10"], rwidth=0.8,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	130 color=["#808080", "#FFFFCC", "#FFBF00", "#DF0101", "#0431B4", "#86B404"],
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	131 stacked=True, alpha=1, align="left", range=(0, maximumX + 1))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	132 maximumY = numpy.amax(p1)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	133 plt.ylim((0, maximumY * 1.2))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	134 plt.ylabel("Absolute Frequency", fontsize=14)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	135 bins = counts[1] # width of bins
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	136 counts = numpy.array(map(int, counts[0][5]))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	137
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	138 plt.legend(loc='upper right', fontsize=14, frameon=True, bbox_to_anchor=(1.45, 1))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	139 plt.suptitle(subtitle, y=1, x=0.5, fontsize=14)
2 316fbf91dd12 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit f9d5547849dabb59a33a5e998bda4730323d62a9 mheinzl parents: 1 diff changeset	140 plt.xlabel(xlabel, fontsize=14)
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	141 plt.grid(b=True, which='major', color='#424242', linestyle=':')
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	142 plt.xlim((minimumX - step, maximumX + step))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	143 # plt.axis((minimumX - step, maximumX + step, 0, numpy.amax(counts) + sum(counts) * 0.1))
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	144 plt.xticks(numpy.arange(0, maximumX + step, step))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	145
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	146 if nr_above_bars:
14 883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e mheinzl parents: 13 diff changeset	147 bin_centers = -0.4 * numpy.diff(bins) + bins[:-1]
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e mheinzl parents: 13 diff changeset	148 for x_label, label in zip(counts, bin_centers): # labels for values
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e mheinzl parents: 13 diff changeset	149 if x_label == 0:
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e mheinzl parents: 13 diff changeset	150 continue
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e mheinzl parents: 13 diff changeset	151 else:
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	152 if rel_freq:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	153 plt.annotate("{:,}\n{:.3f}".format(int(round(x_label * len(numpy.concatenate(list1)))),
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	154 float(x_label)),
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	155 xy=(label, x_label + len(numpy.concatenate(list1)) * 0.0001),
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	156 xycoords="data", color="#000066", fontsize=10)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	157 else:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	158 plt.annotate("{:,}\n{:.3f}".format(x_label, float(x_label) / sum(counts)),
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	159 xy=(label, x_label + len(numpy.concatenate(list1)) * 0.01),
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	160 xycoords="data", color="#000066", fontsize=10)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	161
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	162 if nr_unique_chimeras != 0:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	163 if (relative and ((counts[len(counts)-1] / nr_unique_chimeras) == 2)) or \
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	164 (sum(counts) / nr_unique_chimeras) == 2:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	165 legend = "nr. of tags = {:,}\nsample size = {:,}\nnr. of data points = {:,}\nnr. of CF = {:,} ({:,})"\
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	166 .format(lenTags, len_sample, len(numpy.concatenate(list1)), nr_unique_chimeras, nr_unique_chimeras * 2)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	167 else:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	168 legend = "nr. of tags = {:,}\nsample size = {:,}\nnr. of data points = {:,}\nnr. of CF = {:,}".format(
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	169 lenTags, len_sample, len(numpy.concatenate(list1)), nr_unique_chimeras)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	170 else:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	171 legend = "nr. of tags = {:,}\nsample size = {:,}\nnr. of data points = {:,}".format(
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	172 lenTags, len_sample, len(numpy.concatenate(list1)))
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	173
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	174 plt.text(0.14, -0.07, legend, size=12, transform=plt.gcf().transFigure)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	175 pdf.savefig(fig, bbox_inches="tight")
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	176 plt.close("all")
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	177 plt.clf()
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	178
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	179
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	180 def plotHDwithDCS(list1, maximumX, minimumX, subtitle, lenTags, pdf, xlabel, relative=False,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	181 nr_above_bars=True, nr_unique_chimeras=0, len_sample=0, rel_freq=False):
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	182 step = 1
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	183 fig = plt.figure(figsize=(6, 8))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	184 plt.subplots_adjust(bottom=0.1)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	185 p1 = numpy.array([v for k, v in sorted(Counter(numpy.concatenate(list1)).iteritems())])
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	186 maximumY = numpy.amax(p1)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	187 bin1 = maximumX + 1
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	188 if rel_freq:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	189 w = [numpy.zeros_like(data) + 1. / len(numpy.concatenate(list1)) for data in list1]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	190 counts = plt.hist(list1, bins=bin1, edgecolor='black', linewidth=1, weights=w,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	191 label=["DCS", "ab", "ba"], rwidth=0.8, color=["#FF0000", "#5FB404", "#FFBF00"],
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	192 stacked=True, alpha=1, align="left", range=(0, maximumX + 1))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	193 plt.ylim((0, (float(maximumY) / sum(p1)) * 1.2))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	194 plt.ylabel("Relative Frequency", fontsize=14)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	195 bins = counts[1] # width of bins
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	196 counts = numpy.array(map(float, counts[0][2]))
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	197
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	198 else:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	199 counts = plt.hist(list1, bins=bin1, edgecolor='black', linewidth=1,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	200 label=["DCS", "ab", "ba"], rwidth=0.8, color=["#FF0000", "#5FB404", "#FFBF00"],
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	201 stacked=True, alpha=1, align="left", range=(0, maximumX + 1))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	202 plt.ylim((0, maximumY * 1.2))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	203 plt.ylabel("Absolute Frequency", fontsize=14)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	204 bins = counts[1] # width of bins
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	205 counts = numpy.array(map(int, counts[0][2]))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	206
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	207 plt.legend(loc='upper right', fontsize=14, frameon=True, bbox_to_anchor=(1.45, 1))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	208 plt.suptitle(subtitle, y=1, x=0.5, fontsize=14)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	209 plt.xlabel(xlabel, fontsize=14)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	210 plt.grid(b=True, which='major', color='#424242', linestyle=':')
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	211 plt.xlim((minimumX - step, maximumX + step))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	212 # plt.axis((minimumX - step, maximumX + step, 0, numpy.amax(counts) + sum(counts) * 0.1))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	213 plt.xticks(numpy.arange(0, maximumX + step, step))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	214
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	215 if nr_above_bars:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	216 bin_centers = -0.4 * numpy.diff(bins) + bins[:-1]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	217 for x_label, label in zip(counts, bin_centers): # labels for values
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	218 if x_label == 0:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	219 continue
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	220 else:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	221 if rel_freq:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	222 plt.annotate("{:,}\n{:.3f}".format(int(round(x_label * len(numpy.concatenate(list1)))),
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	223 float(x_label)),
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	224 xy=(label, x_label + len(numpy.concatenate(list1)) * 0.0001),
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	225 xycoords="data", color="#000066", fontsize=10)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	226 else:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	227 plt.annotate("{:,}\n{:.3f}".format(x_label, float(x_label) / sum(counts)),
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	228 xy=(label, x_label + len(numpy.concatenate(list1)) * 0.01),
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	229 xycoords="data", color="#000066", fontsize=10)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	230
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	231 if nr_unique_chimeras != 0:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	232 if (sum(counts) / nr_unique_chimeras) == 2:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	233 legend = "nr. of tags = {:,}\nsample size = {:,}\nnr. of data points = {:,}\nnr. of CF = {:,} ({:,})".\
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	234 format(lenTags, len_sample, len(numpy.concatenate(list1)), nr_unique_chimeras, nr_unique_chimeras * 2)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	235 else:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	236 legend = "nr. of tags = {:,}\nsample size = {:,}\nnr. of data points = {:,}\nnr. of CF = {:,}".format(
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	237 lenTags, len_sample, len(numpy.concatenate(list1)), nr_unique_chimeras)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	238 else:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	239 legend = "nr. of tags = {:,}\nsample size = {:,}\nnr. of data points = {:,}".format(
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	240 lenTags, len_sample, len(numpy.concatenate(list1)))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	241 plt.text(0.14, -0.07, legend, size=12, transform=plt.gcf().transFigure)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	242
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	243 legend2 = "SSCS ab = {:,}\nSSCS ba = {:,}\nDCS = {:,}".format(len(list1[1]), len(list1[2]), len(list1[0]))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	244 plt.text(0.6, -0.047, legend2, size=12, transform=plt.gcf().transFigure)
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	245
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	246 pdf.savefig(fig, bbox_inches="tight")
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	247 plt.close("all")
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	248 plt.clf()
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	249
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	250
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	251 def plotHDwithinSeq(sum1, sum1min, sum2, sum2min, min_value, lenTags, pdf, len_sample, rel_freq=False):
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	252 fig = plt.figure(figsize=(6, 8))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	253 plt.subplots_adjust(bottom=0.1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	254
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	255 ham_partial = [sum1, sum1min, sum2, sum2min, numpy.array(min_value)] # new hd within tags
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	256 maximumX = numpy.amax(numpy.concatenate(ham_partial))
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	257 minimumX = numpy.amin(numpy.concatenate(ham_partial))
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	258 maximumY = numpy.amax(numpy.array(numpy.concatenate(map(lambda x: numpy.bincount(x), ham_partial))))
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	259
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	260 if len(range(minimumX, maximumX)) == 0:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	261 range1 = minimumX
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	262 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	263 range1 = range(minimumX, maximumX + 2)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	264
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	265 if rel_freq:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	266 w = [numpy.zeros_like(data) + 1. / len(data) for data in ham_partial]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	267 plt.hist(ham_partial, align="left", rwidth=0.8, stacked=False, weights=w,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	268 label=["HD a", "HD b'", "HD b", "HD a'", "HD a+b', a'+b"],
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	269 bins=range1, color=["#58ACFA", "#0404B4", "#FE642E", "#B40431", "#585858"],
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	270 edgecolor='black', linewidth=1)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	271 plt.ylabel("Relative Frequency", fontsize=14)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	272 # plt.ylim(-0.1, (float(maximumY) / len(numpy.concatenate(ham_partial))) * 1.2)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	273 else:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	274 plt.hist(ham_partial, align="left", rwidth=0.8, stacked=False,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	275 label=["HD a", "HD b'", "HD b", "HD a'", "HD a+b', a'+b"],
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	276 bins=range1, color=["#58ACFA", "#0404B4", "#FE642E", "#B40431", "#585858"],
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	277 edgecolor='black', linewidth=1)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	278 plt.ylabel("Absolute Frequency", fontsize=14)
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	279
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	280 plt.legend(loc='upper right', fontsize=14, frameon=True, bbox_to_anchor=(1.55, 1))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	281 plt.suptitle('Hamming distances within tags', fontsize=14)
14 883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e mheinzl parents: 13 diff changeset	282 plt.xlabel("HD", fontsize=14)
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	283 plt.grid(b=True, which='major', color='#424242', linestyle=':')
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	284 plt.xlim((minimumX - 1, maximumX + 1))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	285 # plt.axis((minimumX - 1, maximumX + 1, 0, maximumY * 1.2))
2 316fbf91dd12 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit f9d5547849dabb59a33a5e998bda4730323d62a9 mheinzl parents: 1 diff changeset	286 plt.xticks(numpy.arange(0, maximumX + 1, 1.0))
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	287 legend = "nr. of tags = {:,}\nsample size = {:,}\nnr. of data points = {:,}".format(
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	288 lenTags, len_sample, len(numpy.concatenate(ham_partial)))
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	289 plt.text(0.14, -0.05, legend, size=12, transform=plt.gcf().transFigure)
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	290 pdf.savefig(fig, bbox_inches="tight")
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	291 plt.close("all")
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	292 plt.clf()
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	293
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	294
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	295 def createTableFSD2(list1, diff=True):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	296 selfAB = numpy.concatenate(list1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	297 uniqueFS = numpy.unique(selfAB)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	298 nr = numpy.arange(0, len(uniqueFS), 1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	299 if diff is False:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	300 count = numpy.zeros((len(uniqueFS), 6))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	301 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	302 count = numpy.zeros((len(uniqueFS), 7))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	303 state = 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	304 for i in list1:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	305 counts = list(Counter(i).items())
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	306 hd = [item[0] for item in counts]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	307 c = [item[1] for item in counts]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	308 table = numpy.column_stack((hd, c))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	309 if len(table) == 0:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	310 state = state + 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	311 continue
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	312 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	313 if state == 1:
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	314 for k, l in zip(uniqueFS, nr):
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	315 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	316 if j[0] == uniqueFS[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	317 count[l, 0] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	318 if state == 2:
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	319 for k, l in zip(uniqueFS, nr):
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	320 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	321 if j[0] == uniqueFS[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	322 count[l, 1] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	323 if state == 3:
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	324 for k, l in zip(uniqueFS, nr):
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	325 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	326 if j[0] == uniqueFS[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	327 count[l, 2] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	328 if state == 4:
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	329 for k, l in zip(uniqueFS, nr):
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	330 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	331 if j[0] == uniqueFS[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	332 count[l, 3] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	333 if state == 5:
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	334 for k, l in zip(uniqueFS, nr):
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	335 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	336 if j[0] == uniqueFS[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	337 count[l, 4] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	338 if state == 6:
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	339 for k, l in zip(uniqueFS, nr):
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	340 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	341 if j[0] == uniqueFS[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	342 count[l, 5] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	343 if state == 7:
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	344 for k, l in zip(uniqueFS, nr):
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	345 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	346 if j[0] == uniqueFS[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	347 count[l, 6] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	348 state = state + 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	349 sumRow = count.sum(axis=1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	350 sumCol = count.sum(axis=0)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	351 uniqueFS = uniqueFS.astype(str)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	352 if uniqueFS[len(uniqueFS) - 1] == "20":
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	353 uniqueFS[len(uniqueFS) - 1] = ">20"
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	354 first = ["FS={}".format(i) for i in uniqueFS]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	355 final = numpy.column_stack((first, count, sumRow))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	356 return (final, sumCol)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	357
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	358
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	359 def createFileFSD2(summary, sumCol, overallSum, output_file, name, sep, rel=False, diff=True):
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	360 output_file.write(name)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	361 output_file.write("\n")
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	362 if diff is False:
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	363 output_file.write("{}HD=1{}HD=2{}HD=3{}HD=4{}HD=5-8{}HD>8{}sum{}\n".format(
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	364 sep, sep, sep, sep, sep, sep, sep, sep))
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	365 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	366 if rel is False:
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	367 output_file.write("{}diff=0{}diff=1{}diff=2{}diff=3{}diff=4{}diff=5-8{}diff>8{}sum{}\n".format(
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	368 sep, sep, sep, sep, sep, sep, sep, sep, sep))
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	369 else:
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	370 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".
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	371 format(sep, sep, sep, sep, sep, sep, sep, sep, sep))
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	372 for item in summary:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	373 for nr in item:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	374 if "FS" not in nr and "diff" not in nr:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	375 nr = nr.astype(float)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	376 nr = nr.astype(int)
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	377 output_file.write("{}{}".format(nr, sep))
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	378 output_file.write("\n")
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	379 output_file.write("sum{}".format(sep))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	380 sumCol = map(int, sumCol)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	381 for el in sumCol:
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	382 output_file.write("{}{}".format(el, sep))
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	383 output_file.write("{}{}".format(overallSum.astype(int), sep))
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	384 output_file.write("\n\n")
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	385
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	386
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	387 def createTableHD(list1, row_label):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	388 selfAB = numpy.concatenate(list1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	389 uniqueHD = numpy.unique(selfAB)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	390 nr = numpy.arange(0, len(uniqueHD), 1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	391 count = numpy.zeros((len(uniqueHD), 6))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	392 state = 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	393 for i in list1:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	394 counts = list(Counter(i).items())
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	395 hd = [item[0] for item in counts]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	396 c = [item[1] for item in counts]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	397 table = numpy.column_stack((hd, c))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	398 if len(table) == 0:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	399 state = state + 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	400 continue
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	401 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	402 if state == 1:
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	403 for k, l in zip(uniqueHD, nr):
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	404 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	405 if j[0] == uniqueHD[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	406 count[l, 0] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	407 if state == 2:
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	408 for k, l in zip(uniqueHD, nr):
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	409 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	410 if j[0] == uniqueHD[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	411 count[l, 1] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	412 if state == 3:
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	413 for k, l in zip(uniqueHD, nr):
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	414 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	415 if j[0] == uniqueHD[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	416 count[l, 2] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	417 if state == 4:
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	418 for k, l in zip(uniqueHD, nr):
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	419 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	420 if j[0] == uniqueHD[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	421 count[l, 3] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	422 if state == 5:
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	423 for k, l in zip(uniqueHD, nr):
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	424 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	425 if j[0] == uniqueHD[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	426 count[l, 4] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	427 if state == 6:
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	428 for k, l in zip(uniqueHD, nr):
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	429 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	430 if j[0] == uniqueHD[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	431 count[l, 5] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	432 state = state + 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	433 sumRow = count.sum(axis=1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	434 sumCol = count.sum(axis=0)
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	435 first = ["{}{}".format(row_label, i) for i in uniqueHD]
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	436 final = numpy.column_stack((first, count, sumRow))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	437 return (final, sumCol)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	438
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	439
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	440 def createTableHDwithTags(list1):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	441 selfAB = numpy.concatenate(list1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	442 uniqueHD = numpy.unique(selfAB)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	443 nr = numpy.arange(0, len(uniqueHD), 1)
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	444 count = numpy.zeros((len(uniqueHD), 5))
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	445 state = 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	446 for i in list1:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	447 counts = list(Counter(i).items())
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	448 hd = [item[0] for item in counts]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	449 c = [item[1] for item in counts]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	450 table = numpy.column_stack((hd, c))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	451 if len(table) == 0:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	452 state = state + 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	453 continue
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	454 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	455 if state == 1:
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	456 for k, l in zip(uniqueHD, nr):
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	457 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	458 if j[0] == uniqueHD[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	459 count[l, 0] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	460 if state == 2:
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	461 for k, l in zip(uniqueHD, nr):
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	462 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	463 if j[0] == uniqueHD[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	464 count[l, 1] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	465 if state == 3:
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	466 for k, l in zip(uniqueHD, nr):
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	467 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	468 if j[0] == uniqueHD[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	469 count[l, 2] = j[1]
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	470 if state == 4:
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	471 for k, l in zip(uniqueHD, nr):
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	472 for j in table:
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	473 if j[0] == uniqueHD[l]:
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	474 count[l, 3] = j[1]
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	475 if state == 5:
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	476 for k, l in zip(uniqueHD, nr):
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	477 for j in table:
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	478 if j[0] == uniqueHD[l]:
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	479 count[l, 4] = j[1]
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	480 state = state + 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	481 sumRow = count.sum(axis=1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	482 sumCol = count.sum(axis=0)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	483 first = ["HD={}".format(i) for i in uniqueHD]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	484 final = numpy.column_stack((first, count, sumRow))
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	485 return (final, sumCol)
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	486
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	487
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	488 def createTableHDwithDCS(list1):
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	489 selfAB = numpy.concatenate(list1)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	490 uniqueHD = numpy.unique(selfAB)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	491 nr = numpy.arange(0, len(uniqueHD), 1)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	492 count = numpy.zeros((len(uniqueHD), len(list1)))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	493 state = 1
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	494 for i in list1:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	495 counts = list(Counter(i).items())
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	496 hd = [item[0] for item in counts]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	497 c = [item[1] for item in counts]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	498 table = numpy.column_stack((hd, c))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	499 if len(table) == 0:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	500 state = state + 1
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	501 continue
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	502 else:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	503 if state == 1:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	504 for k, l in zip(uniqueHD, nr):
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	505 for j in table:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	506 if j[0] == uniqueHD[l]:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	507 count[l, 0] = j[1]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	508 if state == 2:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	509 for k, l in zip(uniqueHD, nr):
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	510 for j in table:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	511 if j[0] == uniqueHD[l]:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	512 count[l, 1] = j[1]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	513 if state == 3:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	514 for k, l in zip(uniqueHD, nr):
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	515 for j in table:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	516 if j[0] == uniqueHD[l]:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	517 count[l, 2] = j[1]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	518 state = state + 1
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	519 sumRow = count.sum(axis=1)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	520 sumCol = count.sum(axis=0)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	521 first = ["HD={}".format(i) for i in uniqueHD]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	522 final = numpy.column_stack((first, count, sumRow))
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	523 return (final, sumCol)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	524
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	525
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	526 def createFileHD(summary, sumCol, overallSum, output_file, name, sep):
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	527 output_file.write(name)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	528 output_file.write("\n")
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	529 output_file.write("{}FS=1{}FS=2{}FS=3{}FS=4{}FS=5-10{}FS>10{}sum{}\n".format(
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	530 sep, sep, sep, sep, sep, sep, sep, sep))
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	531 for item in summary:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	532 for nr in item:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	533 if "HD" not in nr and "diff" not in nr:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	534 nr = nr.astype(float)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	535 nr = nr.astype(int)
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	536 output_file.write("{}{}".format(nr, sep))
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	537 output_file.write("\n")
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	538 output_file.write("sum{}".format(sep))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	539 sumCol = map(int, sumCol)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	540 for el in sumCol:
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	541 output_file.write("{}{}".format(el, sep))
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	542 output_file.write("{}{}".format(overallSum.astype(int), sep))
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	543 output_file.write("\n\n")
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	544
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	545
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	546 def createFileHDwithDCS(summary, sumCol, overallSum, output_file, name, sep):
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	547 output_file.write(name)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	548 output_file.write("\n")
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	549 output_file.write("{}DCS{}SSCS ab{}SSCS ba{}sum{}\n".format(sep, sep, sep, sep, sep))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	550 for item in summary:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	551 for nr in item:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	552 if "HD" not in nr:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	553 nr = nr.astype(float)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	554 nr = nr.astype(int)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	555 output_file.write("{}{}".format(nr, sep))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	556 output_file.write("\n")
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	557 output_file.write("sum{}".format(sep))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	558 sumCol = map(int, sumCol)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	559 for el in sumCol:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	560 output_file.write("{}{}".format(el, sep))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	561 output_file.write("{}{}".format(overallSum.astype(int), sep))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	562 output_file.write("\n\n")
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	563
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	564
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	565 def createFileHDwithinTag(summary, sumCol, overallSum, output_file, name, sep):
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	566 output_file.write(name)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	567 output_file.write("\n")
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	568 output_file.write("{}HD DCS{}HD b'{}HD b{}HD a'{}HD a+b', a'+b{}sum{}\n".format(sep, sep, sep, sep, sep, sep, sep))
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	569 for item in summary:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	570 for nr in item:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	571 if "HD" not in nr:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	572 nr = nr.astype(float)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	573 nr = nr.astype(int)
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	574 output_file.write("{}{}".format(nr, sep))
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	575 output_file.write("\n")
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	576 output_file.write("sum{}".format(sep))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	577 sumCol = map(int, sumCol)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	578 for el in sumCol:
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	579 output_file.write("{}{}".format(el, sep))
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	580 output_file.write("{}{}".format(overallSum.astype(int), sep))
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	581 output_file.write("\n\n")
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	582
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	583
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	584 def hamming(array1, array2):
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	585 res = 99 * numpy.ones(len(array1))
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	586 i = 0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	587 array2 = numpy.unique(array2) # remove duplicate sequences to decrease running time
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	588 for a in array1:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	589 dist = numpy.array([sum(itertools.imap(operator.ne, a, b)) for b in array2]) # fastest
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	590 res[i] = numpy.amin(dist[dist > 0]) # pick min distance greater than zero
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	591 i += 1
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	592 return res
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	593
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	594
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	595 def hamming_difference(array1, array2, mate_b):
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	596 array2 = numpy.unique(array2) # remove duplicate sequences to decrease running time
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	597 array1_half = numpy.array([i[0:(len(i)) / 2] for i in array1]) # mate1 part1
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	598 array1_half2 = numpy.array([i[len(i) / 2:len(i)] for i in array1]) # mate1 part 2
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	599 array2_half = numpy.array([i[0:(len(i)) / 2] for i in array2]) # mate2 part1
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	600 array2_half2 = numpy.array([i[len(i) / 2:len(i)] for i in array2]) # mate2 part2
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	601
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	602 # diff11 = 999 * numpy.ones(len(array2))
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	603 # relativeDiffList = 999 * numpy.ones(len(array2))
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	604 # ham1 = 999 * numpy.ones(len(array2))
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	605 # ham2 = 999 * numpy.ones(len(array2))
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	606 # min_valueList = 999 * numpy.ones(len(array2))
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	607 # min_tagsList = 999 * numpy.ones(len(array2))
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	608 # diff11_zeros = 999 * numpy.ones(len(array2))
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	609 # min_tagsList_zeros = 999 * numpy.ones(len(array2))
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	610
8 e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a mheinzl parents: 7 diff changeset	611 diff11 = []
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a mheinzl parents: 7 diff changeset	612 relativeDiffList = []
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a mheinzl parents: 7 diff changeset	613 ham1 = []
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a mheinzl parents: 7 diff changeset	614 ham2 = []
14 883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e mheinzl parents: 13 diff changeset	615 ham1min = []
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e mheinzl parents: 13 diff changeset	616 ham2min = []
8 e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a mheinzl parents: 7 diff changeset	617 min_valueList = []
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a mheinzl parents: 7 diff changeset	618 min_tagsList = []
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a mheinzl parents: 7 diff changeset	619 diff11_zeros = []
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a mheinzl parents: 7 diff changeset	620 min_tagsList_zeros = []
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	621 max_tag_list = []
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	622 i = 0 # counter, only used to see how many HDs of tags were already calculated
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	623 if mate_b is False: # HD calculation for all a's
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	624 half1_mate1 = array1_half
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	625 half2_mate1 = array1_half2
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	626 half1_mate2 = array2_half
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	627 half2_mate2 = array2_half2
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	628 elif mate_b is True: # HD calculation for all b's
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	629 half1_mate1 = array1_half2
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	630 half2_mate1 = array1_half
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	631 half1_mate2 = array2_half2
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	632 half2_mate2 = array2_half
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	633
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	634 # half1_mate1, index_halves = numpy.unique(half1_mate1, return_index=True)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	635 # print(len(half1_mate1))
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	636 # half2_mate1 = half2_mate1[index_halves]
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	637 # array1 = array1[index_halves]
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	638
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	639 for a, b, tag in zip(half1_mate1, half2_mate1, array1):
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	640 # exclude identical tag from array2, to prevent comparison to itself
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	641 sameTag = numpy.where(array2 == tag)[0]
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	642 indexArray2 = numpy.arange(0, len(array2), 1)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	643 index_withoutSame = numpy.delete(indexArray2, sameTag) # delete identical tag from the data
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	644
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	645 # all tags without identical tag
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	646 array2_half_withoutSame = half1_mate2[index_withoutSame]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	647 array2_half2_withoutSame = half2_mate2[index_withoutSame]
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	648 array2_withoutSame = array2[index_withoutSame] # whole tag (=not splitted into 2 halfs)
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	649 # calculate HD of "a" in the tag to all "a's" or "b" in the tag to all "b's"
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	650 dist = numpy.array([sum(itertools.imap(operator.ne, a, c)) for c in
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	651 array2_half_withoutSame])
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	652 min_index = numpy.where(dist == dist.min())[0] # get index of min HD
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	653 min_value = dist.min()
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	654 # min_value = dist[min_index] # get minimum HDs
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	655 # get all "b's" of the tag or all "a's" of the tag with minimum HD
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	656 min_tag_half2 = array2_half2_withoutSame[min_index]
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	657 min_tag_array2 = array2_withoutSame[min_index] # get whole tag with min HD
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	658
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	659 dist_second_half = numpy.array([sum(itertools.imap(operator.ne, b, e)) for e in
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	660 min_tag_half2]) # calculate HD of "b" to all "b's" or "a" to all "a's"
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	661 max_value = dist_second_half.max()
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	662 max_index = numpy.where(dist_second_half == dist_second_half.max())[0] # get index of max HD
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	663 max_tag = min_tag_array2[max_index]
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	664
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	665 # for d, d2 in zip(min_value, max_value):
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	666 if mate_b is True: # half2, corrects the variable of the HD from both halfs if it is a or b
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	667 ham2.append(min_value)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	668 ham2min.append(max_value)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	669 else: # half1, corrects the variable of the HD from both halfs if it is a or b
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	670 ham1.append(min_value)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	671 ham1min.append(max_value)
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	672
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	673 min_valueList.append(min_value + max_value)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	674 min_tagsList.append(tag)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	675 difference1 = abs(min_value - max_value)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	676 diff11.append(difference1)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	677 rel_difference = round(float(difference1) / (min_value + max_value), 1)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	678 relativeDiffList.append(rel_difference)
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	679
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	680 # tags which have identical parts:
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	681 if min_value == 0 or max_value == 0:
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	682 min_tagsList_zeros.append(numpy.array(tag))
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	683 difference1_zeros = abs(min_value - max_value) # hd of non-identical part
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	684 diff11_zeros.append(difference1_zeros)
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	685 max_tag_list.append(numpy.array(max_tag))
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	686 else:
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	687 min_tagsList_zeros.append(None)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	688 diff11_zeros.append(None)
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	689 max_tag_list.append(None)
8 e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a mheinzl parents: 7 diff changeset	690 i += 1
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	691
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	692 # print(i)
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	693 # diff11 = [st for st in diff11 if st != 999]
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	694 # ham1 = [st for st in ham1 if st != 999]
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	695 # ham2 = [st for st in ham2 if st != 999]
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	696 # min_valueList = [st for st in min_valueList if st != 999]
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	697 # min_tagsList = [st for st in min_tagsList if st != 999]
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	698 # relativeDiffList = [st for st in relativeDiffList if st != 999]
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	699 # diff11_zeros = [st for st in diff11_zeros if st != 999]
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	700 # min_tagsList_zeros = [st for st in min_tagsList_zeros if st != 999]
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	701 return ([diff11, ham1, ham2, min_valueList, min_tagsList, relativeDiffList, diff11_zeros,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	702 min_tagsList_zeros, ham1min, ham2min, max_tag_list])
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	703
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	704
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	705 def readFileReferenceFree(file):
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	706 with open(file, 'r') as dest_f:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	707 data_array = numpy.genfromtxt(dest_f, skip_header=0, delimiter='\t', comments='#', dtype='string')
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	708 integers = numpy.array(data_array[:, 0]).astype(int)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	709 return(integers, data_array)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	710
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	711
11 7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9 mheinzl parents: 10 diff changeset	712 def hammingDistanceWithFS(fs, ham):
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9 mheinzl parents: 10 diff changeset	713 fs = numpy.asarray(fs)
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	714 maximum = max(ham)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	715 minimum = min(ham)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	716 ham = numpy.asarray(ham)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	717
11 7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9 mheinzl parents: 10 diff changeset	718 singletons = numpy.where(fs == 1)[0]
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	719 data = ham[singletons]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	720
11 7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9 mheinzl parents: 10 diff changeset	721 hd2 = numpy.where(fs == 2)[0]
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	722 data2 = ham[hd2]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	723
11 7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9 mheinzl parents: 10 diff changeset	724 hd3 = numpy.where(fs == 3)[0]
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	725 data3 = ham[hd3]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	726
11 7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9 mheinzl parents: 10 diff changeset	727 hd4 = numpy.where(fs == 4)[0]
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	728 data4 = ham[hd4]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	729
11 7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9 mheinzl parents: 10 diff changeset	730 hd5 = numpy.where((fs >= 5) & (fs <= 10))[0]
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	731 data5 = ham[hd5]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	732
11 7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9 mheinzl parents: 10 diff changeset	733 hd6 = numpy.where(fs > 10)[0]
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	734 data6 = ham[hd6]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	735
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	736 list1 = [data, data2, data3, data4, data5, data6]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	737 return(list1, maximum, minimum)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	738
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	739
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	740 def familySizeDistributionWithHD(fs, ham, diff=False, rel=True):
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	741 hammingDistances = numpy.unique(ham)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	742 fs = numpy.asarray(fs)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	743 ham = numpy.asarray(ham)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	744 bigFamilies2 = numpy.where(fs > 19)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	745 if len(bigFamilies2) != 0:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	746 fs[bigFamilies2] = 20
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	747 maximum = max(fs)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	748 minimum = min(fs)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	749 if diff is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	750 hd0 = numpy.where(ham == 0)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	751 data0 = fs[hd0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	752
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	753 if rel is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	754 hd1 = numpy.where(ham == 0.1)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	755 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	756 hd1 = numpy.where(ham == 1)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	757 data = fs[hd1]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	758
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	759 if rel is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	760 hd2 = numpy.where(ham == 0.2)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	761 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	762 hd2 = numpy.where(ham == 2)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	763 data2 = fs[hd2]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	764
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	765 if rel is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	766 hd3 = numpy.where(ham == 0.3)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	767 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	768 hd3 = numpy.where(ham == 3)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	769 data3 = fs[hd3]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	770
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	771 if rel is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	772 hd4 = numpy.where(ham == 0.4)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	773 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	774 hd4 = numpy.where(ham == 4)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	775 data4 = fs[hd4]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	776
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	777 if rel is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	778 hd5 = numpy.where((ham >= 0.5) & (ham <= 0.8))[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	779 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	780 hd5 = numpy.where((ham >= 5) & (ham <= 8))[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	781 data5 = fs[hd5]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	782
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	783 if rel is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	784 hd6 = numpy.where(ham > 0.8)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	785 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	786 hd6 = numpy.where(ham > 8)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	787 data6 = fs[hd6]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	788
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	789 if diff is True:
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	790 list1 = [data0, data, data2, data3, data4, data5, data6]
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	791 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	792 list1 = [data, data2, data3, data4, data5, data6]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	793
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	794 return(list1, hammingDistances, maximum, minimum)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	795
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	796
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	797 def hammingDistanceWithDCS(minHD_tags_zeros, diff_zeros, data_array):
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	798 diff_zeros = numpy.array(diff_zeros)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	799 maximum = numpy.amax(diff_zeros)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	800 minimum = numpy.amin(diff_zeros)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	801 minHD_tags_zeros = numpy.array(minHD_tags_zeros)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	802
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	803 idx = numpy.concatenate([numpy.where(data_array[:, 1] == i)[0] for i in minHD_tags_zeros])
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	804 subset_data = data_array[idx, :]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	805
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	806 seq = numpy.array(subset_data[:, 1])
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	807
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	808 # find all unique tags and get the indices for ALL tags, but only once
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	809 u, index_unique, c = numpy.unique(numpy.array(seq), return_counts=True, return_index=True)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	810 DCS_tags = u[c == 2]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	811 rest_tags = u[c == 1]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	812
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	813 dcs = numpy.repeat("DCS", len(DCS_tags))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	814 idx_sscs = numpy.concatenate([numpy.where(subset_data[:, 1] == i)[0] for i in rest_tags])
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	815 sscs = subset_data[idx_sscs, 2]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	816
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	817 all_tags = numpy.column_stack((numpy.concatenate((DCS_tags, subset_data[idx_sscs, 1])),
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	818 numpy.concatenate((dcs, sscs))))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	819 hd_DCS = []
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	820 ab_SSCS = []
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	821 ba_SSCS = []
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	822
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	823 for i in range(len(all_tags)):
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	824 tag = all_tags[i, :]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	825 hd = diff_zeros[numpy.where(minHD_tags_zeros == tag[0])[0]]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	826
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	827 if tag[1] == "DCS":
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	828 hd_DCS.append(hd)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	829 elif tag[1] == "ab":
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	830 ab_SSCS.append(hd)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	831 elif tag[1] == "ba":
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	832 ba_SSCS.append(hd)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	833
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	834 if len(hd_DCS) != 0:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	835 hd_DCS = numpy.concatenate(hd_DCS)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	836 if len(ab_SSCS) != 0:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	837 ab_SSCS = numpy.concatenate(ab_SSCS)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	838 if len(ba_SSCS) != 0:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	839 ba_SSCS = numpy.concatenate(ba_SSCS)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	840 list1 = [hd_DCS, ab_SSCS, ba_SSCS] # list for plotting
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	841 return(list1, maximum, minimum)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	842
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	843
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	844 def make_argparser():
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	845 parser = argparse.ArgumentParser(description='Hamming distance analysis of duplex sequencing data')
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	846 parser.add_argument('--inputFile',
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	847 help='Tabular File with three columns: ab or ba, tag and family size.')
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	848 parser.add_argument('--inputName1')
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	849 parser.add_argument('--sample_size', default=1000, type=int,
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	850 help='Sample size of Hamming distance analysis.')
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	851 parser.add_argument('--subset_tag', default=0, type=int,
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	852 help='The tag is shortened to the given number.')
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	853 parser.add_argument('--nproc', default=4, type=int,
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	854 help='The tool runs with the given number of processors.')
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	855 parser.add_argument('--only_DCS', action="store_false",
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	856 help='Only tags of the DCSs are included in the HD analysis')
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	857
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	858 parser.add_argument('--minFS', default=1, type=int,
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	859 help='Only tags, which have a family size greater or equal than specified, '
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	860 'are included in the HD analysis')
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	861 parser.add_argument('--maxFS', default=0, type=int,
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	862 help='Only tags, which have a family size smaller or equal than specified, '
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	863 'are included in the HD analysis')
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	864 parser.add_argument('--nr_above_bars', action="store_true",
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	865 help='If False, values above bars in the histograms are removed')
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	866 parser.add_argument('--rel_freq', action="store_false",
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	867 help='If True, the relative frequencies are displayed.')
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	868
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	869 parser.add_argument('--output_tabular', default="data.tabular", type=str,
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	870 help='Name of the tabular file.')
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	871 parser.add_argument('--output_pdf', default="data.pdf", type=str,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	872 help='Name of the pdf file.')
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	873 parser.add_argument('--output_chimeras_tabular', default="data.tabular", type=str,
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	874 help='Name of the tabular file with all chimeric tags.')
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	875
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	876 return parser
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	877
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	878
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	879 def Hamming_Distance_Analysis(argv):
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	880 # def Hamming_Distance_Analysis(file1, name1, index_size, title_savedFile_pdf, title_savedFile_csv,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	881 # output_chimeras_tabular, onlyDuplicates, minFS=1, maxFS=0, nr_above_bars=True,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	882 # subset=False, nproc=12, rel_freq=False):
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	883 parser = make_argparser()
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	884 args = parser.parse_args(argv[1:])
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	885 file1 = args.inputFile
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	886 name1 = args.inputName1
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	887 index_size = args.sample_size
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	888 title_savedFile_pdf = args.output_pdf
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	889 title_savedFile_csv = args.output_tabular
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	890 output_chimeras_tabular = args.output_chimeras_tabular
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	891 onlyDuplicates = args.only_DCS
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	892 rel_freq = args.rel_freq
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	893 minFS = args.minFS
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	894 maxFS = args.maxFS
14 883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e mheinzl parents: 13 diff changeset	895 nr_above_bars = args.nr_above_bars
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	896 subset = args.subset_tag
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	897 nproc = args.nproc
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	898 sep = "\t"
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	899
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	900 # input checks
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	901 if index_size < 0:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	902 print("index_size is a negative integer.")
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	903 exit(2)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	904 if nproc <= 0:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	905 print("nproc is smaller or equal zero")
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	906 exit(3)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	907 if subset < 0:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	908 print("subset_tag is smaller or equal zero.")
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	909 exit(5)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	910
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	911 # PLOT
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	912 plt.rcParams['axes.facecolor'] = "E0E0E0" # grey background color
10 69aa17354a6e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit f01678e9bfead9f9e1b54dd9ecf7141f057dd9de mheinzl parents: 9 diff changeset	913 plt.rcParams['xtick.labelsize'] = 14
69aa17354a6e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit f01678e9bfead9f9e1b54dd9ecf7141f057dd9de mheinzl parents: 9 diff changeset	914 plt.rcParams['ytick.labelsize'] = 14
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	915 plt.rcParams['patch.edgecolor'] = "#000000"
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	916 plt.rc('figure', figsize=(11.69, 8.27)) # A4 format
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	917 name1 = name1.split(".tabular")[0]
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	918
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	919 with open(title_savedFile_csv, "w") as output_file, PdfPages(title_savedFile_pdf) as pdf:
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	920 print("dataset: ", name1)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	921 integers, data_array = readFileReferenceFree(file1)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	922 data_array = numpy.array(data_array)
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	923 print("total nr of tags:", len(data_array))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	924
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	925 # filter tags out which contain any other character than ATCG
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	926 valid_bases = ["A", "T", "G", "C"]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	927 tagsToDelete = []
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	928 for idx, t in enumerate(data_array[:, 1]):
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	929 for char in t:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	930 if char not in valid_bases:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	931 tagsToDelete.append(idx)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	932 break
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	933
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	934 if len(tagsToDelete) != 0: # delete tags with N in the tag from data
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	935 print("nr of tags with any other character than A, T, C, G:", len(tagsToDelete),
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	936 float(len(tagsToDelete)) / len(data_array))
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	937 index_whole_array = numpy.arange(0, len(data_array), 1)
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	938 index_withoutN_inTag = numpy.delete(index_whole_array, tagsToDelete)
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	939 data_array = data_array[index_withoutN_inTag, :]
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	940 integers = integers[index_withoutN_inTag]
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	941 print("total nr of filtered tags:", len(data_array))
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	942
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	943 int_f = numpy.array(data_array[:, 0]).astype(int)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	944 data_array = data_array[numpy.where(int_f >= minFS)]
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	945 integers = integers[integers >= minFS]
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	946
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	947 # select family size for tags
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	948 if maxFS > 0:
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	949 int_f2 = numpy.array(data_array[:, 0]).astype(int)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	950 data_array = data_array[numpy.where(int_f2 <= maxFS)]
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	951 integers = integers[integers <= maxFS]
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	952
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	953 if onlyDuplicates is True:
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	954 tags = data_array[:, 2]
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	955 seq = data_array[:, 1]
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	956
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	957 # find all unique tags and get the indices for ALL tags, but only once
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	958 u, index_unique, c = numpy.unique(numpy.array(seq), return_counts=True, return_index=True)
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	959 d = u[c == 2]
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	960
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	961 # get family sizes, tag for duplicates
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	962 duplTags_double = integers[numpy.in1d(seq, d)]
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	963 duplTags = duplTags_double[0::2] # ab of DCS
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	964 duplTagsBA = duplTags_double[1::2] # ba of DCS
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	965
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	966 duplTags_tag = tags[numpy.in1d(seq, d)][0::2] # ab
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	967 duplTags_seq = seq[numpy.in1d(seq, d)][0::2] # ab - tags
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	968
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	969 if minFS > 1:
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	970 duplTags_tag = duplTags_tag[(duplTags >= minFS) & (duplTagsBA >= minFS)]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	971 duplTags_seq = duplTags_seq[(duplTags >= minFS) & (duplTagsBA >= minFS)]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	972 duplTags = duplTags[(duplTags >= minFS) & (duplTagsBA >= minFS)] # ab+ba with FS>=3
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	973
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	974 data_array = numpy.column_stack((duplTags, duplTags_seq))
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	975 data_array = numpy.column_stack((data_array, duplTags_tag))
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	976 integers = numpy.array(data_array[:, 0]).astype(int)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	977 print("DCS in whole dataset", len(data_array))
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	978
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	979 print("min FS", min(integers))
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	980 print("max FS", max(integers))
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	981
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	982 # HD analysis for a subset of the tag
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	983 if subset > 0:
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	984 tag1 = numpy.array([i[0:(len(i)) / 2] for i in data_array[:, 1]])
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	985 tag2 = numpy.array([i[len(i) / 2:len(i)] for i in data_array[:, 1]])
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	986
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	987 flanking_region_float = float((len(tag1[0]) - subset)) / 2
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	988 flanking_region = int(flanking_region_float)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	989 if flanking_region_float % 2 == 0:
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	990 tag1_shorten = numpy.array([i[flanking_region:len(i) - flanking_region] for i in tag1])
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	991 tag2_shorten = numpy.array([i[flanking_region:len(i) - flanking_region] for i in tag2])
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	992 else:
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	993 flanking_region_rounded = int(round(flanking_region, 1))
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	994 flanking_region_rounded_end = len(tag1[0]) - subset - flanking_region_rounded
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	995 tag1_shorten = numpy.array(
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	996 [i[flanking_region:len(i) - flanking_region_rounded_end] for i in tag1])
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	997 tag2_shorten = numpy.array(
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	998 [i[flanking_region:len(i) - flanking_region_rounded_end] for i in tag2])
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	999
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1000 data_array_tag = numpy.array([i + j for i, j in zip(tag1_shorten, tag2_shorten)])
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1001 data_array = numpy.column_stack((data_array[:, 0], data_array_tag, data_array[:, 2]))
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	1002
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1003 print("length of tag= ", len(data_array[0, 1]))
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1004 # select sample: if no size given --> all vs. all comparison
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1005 if index_size == 0:
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1006 result = numpy.arange(0, len(data_array), 1)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1007 else:
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1008 numpy.random.shuffle(data_array)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1009 unique_tags, unique_indices = numpy.unique(data_array[:, 1], return_index=True) # get only unique tags
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1010 result = numpy.random.choice(unique_indices, size=index_size,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1011 replace=False) # array of random sequences of size=index.size
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1012
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1013 # result = numpy.random.choice(len(integers), size=index_size,
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1014 # replace=False) # array of random sequences of size=index.size
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1015 # result = numpy.where(numpy.array(random_tags) == numpy.array(data_array[:,1]))[0]
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	1016
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1017 # with open("index_result.pkl", "wb") as o:
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1018 # pickle.dump(result, o, pickle.HIGHEST_PROTOCOL)
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	1019
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1020 # save counts
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1021 # with open(data_folder + "index_sampleTags1000_Barcode3_DCS.pkl", "wb") as f:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1022 # pickle.dump(result, f, pickle.HIGHEST_PROTOCOL)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1023 # with open(data_folder + "dataArray_sampleTags1000_Barcode3_DCS.pkl", "wb") as f1:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1024 # pickle.dump(data_array, f1, pickle.HIGHEST_PROTOCOL)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1025 #
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1026 # with open(data_folder + "index_sampleTags100.pkl", "rb") as f:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1027 # result = pickle.load(f)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1028 #
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1029 # with open(data_folder + "dataArray_sampleTags100.pkl", "rb") as f1:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1030 # data_array = pickle.load(f1)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1031
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1032 # with open(data_folder + "index_result.txt", "w") as t:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1033 # for text in result:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1034 # t.write("{}\n".format(text))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1035
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1036 # comparison random tags to whole dataset
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1037 result1 = data_array[result, 1] # random tags
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1038 result2 = data_array[:, 1] # all tags
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1039 print("sample size= ", len(result1))
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	1040
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1041 # HD analysis of whole tag
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1042 proc_pool = Pool(nproc)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1043 chunks_sample = numpy.array_split(result1, nproc)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1044 ham = proc_pool.map(partial(hamming, array2=result2), chunks_sample)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1045 proc_pool.close()
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1046 proc_pool.join()
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1047 ham = numpy.concatenate(ham).astype(int)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1048 # with open("HD_whole dataset_{}.txt".format(app_f), "w") as output_file1:
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1049 # for h, tag in zip(ham, result1):
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1050 # output_file1.write("{}\t{}\n".format(tag, h))
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	1051
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1052 # # HD analysis for chimeric reads
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1053 # result2 = data_array_whole_dataset[:,1]
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1054
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1055 proc_pool_b = Pool(nproc)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1056 diff_list_a = proc_pool_b.map(partial(hamming_difference, array2=result2, mate_b=False), chunks_sample)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1057 diff_list_b = proc_pool_b.map(partial(hamming_difference, array2=result2, mate_b=True), chunks_sample)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1058 proc_pool_b.close()
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1059 proc_pool_b.join()
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1060 HDhalf1 = numpy.concatenate((numpy.concatenate([item[1] for item in diff_list_a]),
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1061 numpy.concatenate([item_b[1] for item_b in diff_list_b]))).astype(int)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1062 HDhalf2 = numpy.concatenate((numpy.concatenate([item[2] for item in diff_list_a]),
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1063 numpy.concatenate([item_b[2] for item_b in diff_list_b]))).astype(int)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1064 minHDs = numpy.concatenate((numpy.concatenate([item[3] for item in diff_list_a]),
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1065 numpy.concatenate([item_b[3] for item_b in diff_list_b]))).astype(int)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1066 HDhalf1min = numpy.concatenate((numpy.concatenate([item[8] for item in diff_list_a]),
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1067 numpy.concatenate([item_b[8] for item_b in diff_list_b]))).astype(int)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1068 HDhalf2min = numpy.concatenate((numpy.concatenate([item[9] for item in diff_list_a]),
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1069 numpy.concatenate([item_b[9] for item_b in diff_list_b]))).astype(int)
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	1070
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1071 rel_Diff1 = numpy.concatenate([item[5] for item in diff_list_a])
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1072 rel_Diff2 = numpy.concatenate([item[5] for item in diff_list_b])
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1073 diff1 = numpy.concatenate([item[0] for item in diff_list_a])
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1074 diff2 = numpy.concatenate([item[0] for item in diff_list_b])
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1075
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1076 diff_zeros1 = numpy.concatenate([item[6] for item in diff_list_a])
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1077 diff_zeros2 = numpy.concatenate([item[6] for item in diff_list_b])
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1078 minHD_tags = numpy.concatenate([item[4] for item in diff_list_a])
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1079 minHD_tags_zeros1 = numpy.concatenate([item[7] for item in diff_list_a])
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1080 minHD_tags_zeros2 = numpy.concatenate([item[7] for item in diff_list_b])
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1081
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1082 chimera_tags1 = sum([item[10] for item in diff_list_a], [])
30 46bfbec0f9e6 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 033dd7b750f68e8aa68f327d7d72bd311ddbee4e-dirty mheinzl parents: 29 diff changeset	1083 chimera_tags2 = sum([item[10] for item in diff_list_b], [])
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1084
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1085 rel_Diff = []
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1086 diff_zeros = []
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1087 minHD_tags_zeros = []
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1088 diff = []
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1089 chimera_tags = []
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1090 for d1, d2, rel1, rel2, zeros1, zeros2, tag1, tag2, ctag1, ctag2 in \
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1091 zip(diff1, diff2, rel_Diff1, rel_Diff2, diff_zeros1, diff_zeros2, minHD_tags_zeros1, minHD_tags_zeros2,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1092 chimera_tags1, chimera_tags2):
30 46bfbec0f9e6 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 033dd7b750f68e8aa68f327d7d72bd311ddbee4e-dirty mheinzl parents: 29 diff changeset	1093 relatives = numpy.array([rel1, rel2])
46bfbec0f9e6 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 033dd7b750f68e8aa68f327d7d72bd311ddbee4e-dirty mheinzl parents: 29 diff changeset	1094 absolutes = numpy.array([d1, d2])
46bfbec0f9e6 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 033dd7b750f68e8aa68f327d7d72bd311ddbee4e-dirty mheinzl parents: 29 diff changeset	1095 max_idx = numpy.argmax(relatives)
46bfbec0f9e6 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 033dd7b750f68e8aa68f327d7d72bd311ddbee4e-dirty mheinzl parents: 29 diff changeset	1096 rel_Diff.append(relatives[max_idx])
46bfbec0f9e6 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 033dd7b750f68e8aa68f327d7d72bd311ddbee4e-dirty mheinzl parents: 29 diff changeset	1097 diff.append(absolutes[max_idx])
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1098
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1099 if all(i is not None for i in [zeros1, zeros2]):
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1100 diff_zeros.append(max(zeros1, zeros2))
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1101 minHD_tags_zeros.append(str(tag1))
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1102 tags = [ctag1, ctag2]
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1103 chimera_tags.append(tags)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1104 elif zeros1 is not None and zeros2 is None:
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1105 diff_zeros.append(zeros1)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1106 minHD_tags_zeros.append(str(tag1))
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1107 chimera_tags.append(ctag1)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1108 elif zeros1 is None and zeros2 is not None:
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1109 diff_zeros.append(zeros2)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1110 minHD_tags_zeros.append(str(tag2))
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1111 chimera_tags.append(ctag2)
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1112
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1113 chimera_tags_new = chimera_tags
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1114 data_chimeraAnalysis = numpy.column_stack((minHD_tags_zeros, chimera_tags_new))
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1115 # chimeras_dic = defaultdict(list)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1116 #
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1117 # for t1, t2 in zip(minHD_tags_zeros, chimera_tags_new):
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1118 # if len(t2) >1 and type(t2) is not numpy.ndarray:
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1119 # t2 = numpy.concatenate(t2)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1120 # chimeras_dic[t1].append(t2)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1121
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1122 checked_tags = []
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1123 stat_maxTags = []
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1124
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1125 with open(output_chimeras_tabular, "w") as output_file1:
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1126 output_file1.write("chimera tag\tfamily size, read direction\tsimilar tag with HD=0\n")
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1127 for i in range(len(data_chimeraAnalysis)):
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1128 tag1 = data_chimeraAnalysis[i, 0]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1129
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1130 info_tag1 = data_array[data_array[:, 1] == tag1, :]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1131 fs_tag1 = ["{} {}".format(t[0], t[2]) for t in info_tag1]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1132
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1133 if tag1 in checked_tags: # skip tag if already written to file
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1134 continue
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1135
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1136 sample_half_a = tag1[0:(len(tag1)) / 2]
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1137 sample_half_b = tag1[len(tag1) / 2:len(tag1)]
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1138
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1139 max_tags = data_chimeraAnalysis[i, 1]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1140 if len(max_tags) > 1 and type(max_tags) is not numpy.ndarray:
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1141 max_tags = numpy.concatenate(max_tags)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1142 max_tags = numpy.unique(max_tags)
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1143 stat_maxTags.append(len(max_tags))
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1144
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1145 info_maxTags = [data_array[data_array[:, 1] == t, :] for t in max_tags]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1146
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1147 chimera_half_a = numpy.array([t[0:(len(t)) / 2] for t in max_tags]) # mate1 part1
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1148 chimera_half_b = numpy.array([t[len(t) / 2:len(t)] for t in max_tags]) # mate1 part 2
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1149
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1150 new_format = []
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1151 for j in range(len(max_tags)):
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1152 fs_maxTags = ["{} {}".format(t[0], t[2]) for t in info_maxTags[j]]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1153
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1154 if sample_half_a == chimera_half_a[j]:
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1155 max_tag = "{} {} {}".format(chimera_half_a[j], chimera_half_b[j], ", ".join(fs_maxTags))
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1156 new_format.append(max_tag)
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1157
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1158 elif sample_half_b == chimera_half_b[j]:
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1159 max_tag = "{} {} {}".format(chimera_half_a[j], chimera_half_b[j], ", ".join(fs_maxTags))
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1160 new_format.append(max_tag)
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1161 checked_tags.append(max_tags[j])
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1162
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1163 sample_tag = "{} {}\t{}".format(sample_half_a, sample_half_b, ", ".join(fs_tag1))
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1164 output_file1.write("{}\t{}\n".format(sample_tag, ", ".join(new_format)))
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1165
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1166 checked_tags.append(tag1)
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1167
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1168 output_file1.write(
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1169 "This file contains all tags that were identified as chimeras as the first column and the "
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1170 "corresponding tags which returned a Hamming distance of zero in either the first or the second "
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1171 "half of the sample tag as the second column.\n"
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1172 "The tags were separated by an empty space into their halves and the * marks the identical half.")
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1173 output_file1.write("\n\nStatistics of nr. of tags that returned max. HD (2nd column)\n")
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1174 output_file1.write("minimum\t{}\ttag(s)\n".format(numpy.amin(numpy.array(stat_maxTags))))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1175 output_file1.write("mean\t{}\ttag(s)\n".format(numpy.mean(numpy.array(stat_maxTags))))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1176 output_file1.write("median\t{}\ttag(s)\n".format(numpy.median(numpy.array(stat_maxTags))))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1177 output_file1.write("maximum\t{}\ttag(s)\n".format(numpy.amax(numpy.array(stat_maxTags))))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1178 output_file1.write("sum\t{}\ttag(s)\n".format(numpy.sum(numpy.array(stat_maxTags))))
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1179
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1180 lenTags = len(data_array)
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1181 len_sample = len(result1)
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	1182
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1183 quant = numpy.array(data_array[result, 0]).astype(int) # family size for sample of tags
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1184 seq = numpy.array(data_array[result, 1]) # tags of sample
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1185 ham = numpy.asarray(ham) # HD for sample of tags
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	1186
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1187 if onlyDuplicates is True: # ab and ba strands of DCSs
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1188 quant = numpy.concatenate((quant, duplTagsBA[result]))
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1189 seq = numpy.tile(seq, 2)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1190 ham = numpy.tile(ham, 2)
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1191 diff = numpy.tile(diff, 2)
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1192 rel_Diff = numpy.tile(rel_Diff, 2)
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1193 diff_zeros = numpy.tile(diff_zeros, 2)
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	1194
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1195 nr_chimeric_tags = len(data_chimeraAnalysis)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1196 print("nr of chimeras", nr_chimeric_tags)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1197
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1198 # prepare data for different kinds of plots
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1199 # distribution of FSs separated after HD
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1200 familySizeList1, hammingDistances, maximumXFS, minimumXFS = familySizeDistributionWithHD(quant, ham, rel=False)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1201 list1, maximumX, minimumX = hammingDistanceWithFS(quant, ham) # histogram of HDs separated after FS
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	1202
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1203 # get FS for all tags with min HD of analysis of chimeric reads
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1204 # there are more tags than sample size in the plot, because one tag can have multiple minimas
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1205 if onlyDuplicates:
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1206 seqDic = defaultdict(list)
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1207 for s, q in zip(seq, quant):
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1208 seqDic[s].append(q)
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1209 else:
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1210 seqDic = dict(zip(seq, quant))
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1211
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1212 lst_minHD_tags = []
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1213 for i in minHD_tags:
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1214 lst_minHD_tags.append(seqDic.get(i))
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	1215
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1216 if onlyDuplicates:
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1217 lst_minHD_tags = numpy.concatenate(([item[0] for item in lst_minHD_tags],
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1218 [item_b[1] for item_b in lst_minHD_tags])).astype(int)
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1219 # histogram with absolute and relative difference between HDs of both parts of the tag
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1220 listDifference1, maximumXDifference, minimumXDifference = hammingDistanceWithFS(lst_minHD_tags, diff)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1221 listRelDifference1, maximumXRelDifference, minimumXRelDifference = hammingDistanceWithFS(lst_minHD_tags,
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1222 rel_Diff)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1223 # chimeric read analysis: tags which have HD=0 in one of the halfs
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1224 if len(minHD_tags_zeros) != 0:
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1225 lst_minHD_tags_zeros = []
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1226 for i in minHD_tags_zeros:
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1227 lst_minHD_tags_zeros.append(seqDic.get(i)) # get family size for tags of chimeric reads
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1228 if onlyDuplicates:
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1229 lst_minHD_tags_zeros = numpy.concatenate(([item[0] for item in lst_minHD_tags_zeros],
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1230 [item_b[1] for item_b in lst_minHD_tags_zeros])).astype(int)
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1231
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1232 # histogram with HD of non-identical half
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1233 listDifference1_zeros, maximumXDifference_zeros, minimumXDifference_zeros = hammingDistanceWithFS(
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1234 lst_minHD_tags_zeros, diff_zeros)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1235
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1236 if onlyDuplicates is False:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1237 listDCS_zeros, maximumXDCS_zeros, minimumXDCS_zeros = hammingDistanceWithDCS(minHD_tags_zeros,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1238 diff_zeros, data_array)
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1239
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1240 # plot Hamming Distance with Family size distribution
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1241 plotHDwithFSD(list1=list1, maximumX=maximumX, minimumX=minimumX, pdf=pdf, rel_freq=rel_freq,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1242 subtitle="Hamming distance separated by family size", lenTags=lenTags,
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1243 xlabel="HD", nr_above_bars=nr_above_bars, len_sample=len_sample)
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	1244
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1245 # Plot FSD with separation after
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1246 plotFSDwithHD2(familySizeList1, maximumXFS, minimumXFS, rel_freq=rel_freq,
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1247 originalCounts=quant, subtitle="Family size distribution separated by Hamming distance",
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1248 pdf=pdf, relative=False, diff=False)
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1249
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1250 # Plot HD within tags
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1251 plotHDwithinSeq(HDhalf1, HDhalf1min, HDhalf2, HDhalf2min, minHDs, pdf=pdf, lenTags=lenTags,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1252 rel_freq=rel_freq, len_sample=len_sample)
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	1253
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1254 # Plot difference between HD's separated after FSD
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1255 plotHDwithFSD(listDifference1, maximumXDifference, minimumXDifference, pdf=pdf,
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1256 subtitle="Delta Hamming distance within tags", lenTags=lenTags, rel_freq=rel_freq,
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1257 xlabel="absolute delta HD", relative=False, nr_above_bars=nr_above_bars, len_sample=len_sample)
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	1258
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1259 plotHDwithFSD(listRelDifference1, maximumXRelDifference, minimumXRelDifference, pdf=pdf,
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1260 subtitle="Chimera Analysis: relative delta Hamming distance", lenTags=lenTags, rel_freq=rel_freq,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1261 xlabel="relative delta HD", relative=True, nr_above_bars=nr_above_bars,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1262 nr_unique_chimeras=nr_chimeric_tags, len_sample=len_sample)
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	1263
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1264 # plots for chimeric reads
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1265 if len(minHD_tags_zeros) != 0:
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	1266 # HD
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1267 plotHDwithFSD(listDifference1_zeros, maximumXDifference_zeros, minimumXDifference_zeros, pdf=pdf,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1268 subtitle="Hamming distance of chimeric families (CF)", rel_freq=rel_freq,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1269 lenTags=lenTags, xlabel="HD", relative=False,
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1270 nr_above_bars=nr_above_bars, nr_unique_chimeras=nr_chimeric_tags, len_sample=len_sample)
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1271
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1272 if onlyDuplicates is False:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1273 plotHDwithDCS(listDCS_zeros, maximumXDCS_zeros, minimumXDCS_zeros, pdf=pdf,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1274 subtitle="Hamming distance of chimeric families (CF)", rel_freq=rel_freq,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1275 lenTags=lenTags, xlabel="HD", relative=False,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1276 nr_above_bars=nr_above_bars, nr_unique_chimeras=nr_chimeric_tags, len_sample=len_sample)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1277
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1278 # print all data to a CSV file
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1279 # HD
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1280 summary, sumCol = createTableHD(list1, "HD=")
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1281 overallSum = sum(sumCol) # sum of columns in table
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1282
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1283 # FSD
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1284 summary5, sumCol5 = createTableFSD2(familySizeList1, diff=False)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1285 overallSum5 = sum(sumCol5)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1286
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1287 # HD of both parts of the tag
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1288 summary9, sumCol9 = createTableHDwithTags([HDhalf1, HDhalf1min, HDhalf2, HDhalf2min, numpy.array(minHDs)])
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1289 overallSum9 = sum(sumCol9)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1290
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1291 # HD
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1292 # absolute difference
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1293 summary11, sumCol11 = createTableHD(listDifference1, "diff=")
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1294 overallSum11 = sum(sumCol11)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1295 # relative difference and all tags
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1296 summary13, sumCol13 = createTableHD(listRelDifference1, "diff=")
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1297 overallSum13 = sum(sumCol13)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1298
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1299 # chimeric reads
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1300 if len(minHD_tags_zeros) != 0:
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1301 # absolute difference and tags where at least one half has HD=0
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1302 summary15, sumCol15 = createTableHD(listDifference1_zeros, "HD=")
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1303 overallSum15 = sum(sumCol15)
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	1304
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1305 if onlyDuplicates is False:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1306 summary16, sumCol16 = createTableHDwithDCS(listDCS_zeros)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1307 overallSum16 = sum(sumCol16)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1308
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1309 output_file.write("{}\n".format(name1))
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1310 output_file.write("nr of tags{}{:,}\nsample size{}{:,}\n\n".format(sep, lenTags, sep, len_sample))
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1311
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1312 # HD
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1313 createFileHD(summary, sumCol, overallSum, output_file,
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1314 "Hamming distance separated by family size", sep)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1315 # FSD
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1316 createFileFSD2(summary5, sumCol5, overallSum5, output_file,
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1317 "Family size distribution separated by Hamming distance", sep,
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1318 diff=False)
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	1319
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1320 # output_file.write("{}{}\n".format(sep, name1))
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1321 output_file.write("\n")
21 9919024d7778 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6 mheinzl parents: 20 diff changeset	1322 max_fs = numpy.bincount(integers[result])
9919024d7778 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6 mheinzl parents: 20 diff changeset	1323 output_file.write("max. family size in sample:{}{}\n".format(sep, max(integers[result])))
9919024d7778 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6 mheinzl parents: 20 diff changeset	1324 output_file.write("absolute frequency:{}{}\n".format(sep, max_fs[len(max_fs) - 1]))
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1325 output_file.write(
21 9919024d7778 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6 mheinzl parents: 20 diff changeset	1326 "relative frequency:{}{}\n\n".format(sep, float(max_fs[len(max_fs) - 1]) / sum(max_fs)))
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1327
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1328 # HD within tags
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1329 output_file.write(
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1330 "The Hamming distances were calculated by comparing the first halve against all halves and selected the "
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1331 "minimum value (HD a).\nFor the second half of the tag, we compared them against all tags which resulted "
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1332 "in the minimum HD of the previous step and selected the maximum value (HD b').\nFinally, it was possible "
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1333 "to calculate the absolute and relative differences between the HDs (absolute and relative delta HD).\n"
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1334 "These calculations were repeated, but starting with the second half in the first step to find all "
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1335 "possible chimeras in the data (HD b and HD For simplicity we used the maximum value between the delta "
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1336 "values in the end.\nWhen only tags that can form DCS were allowed in the analysis, family sizes for the "
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1337 "forward and reverse (ab and ba) will be included in the plots.\n")
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1338
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1339 output_file.write("\nlength of one half of the tag{}{}\n\n".format(sep, len(data_array[0, 1]) / 2))
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1340
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1341 createFileHDwithinTag(summary9, sumCol9, overallSum9, output_file,
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1342 "Hamming distance of each half in the tag", sep)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1343 createFileHD(summary11, sumCol11, overallSum11, output_file,
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1344 "Absolute delta Hamming distance within the tag", sep)
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1345
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1346 createFileHD(summary13, sumCol13, overallSum13, output_file,
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1347 "Chimera analysis: relative delta Hamming distance", sep)
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1348
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1349 if len(minHD_tags_zeros) != 0:
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	1350 output_file.write(
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1351 "All tags were filtered: only those tags where at least one half was identical (HD=0) and therefore, "
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1352 "had a relative delta of 1 were kept. These tags are considered as chimeric.\nSo the Hamming distances "
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1353 "of the chimeric tags are shown.\n")
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1354 createFileHD(summary15, sumCol15, overallSum15, output_file,
29 6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1355 "Hamming distance of chimeric families separated after FS", sep)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1356
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1357 if onlyDuplicates is False:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1358 createFileHDwithDCS(summary16, sumCol16, overallSum16, output_file,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty mheinzl parents: 28 diff changeset	1359 "Hamming distance of chimeric families separated after DCS and single SSCS", sep)
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1360
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1361 output_file.write("\n")
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	1362
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	1363
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	1364 if __name__ == '__main__':
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	1365 sys.exit(Hamming_Distance_Analysis(sys.argv))

Mercurial > repos > mheinzl > hd

annotate hd.py @ 30:46bfbec0f9e6 draft