hd: hd.py annotate

annotate hd.py @ 28:1fa7342a140d draft

planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty

author	mheinzl
date	Mon, 03 Jun 2019 05:37:01 -0400
parents	df1fc5cedc8b
children	6b15b3b6405c

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 #
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	8 # Takes at least one TABULAR file with tags before the alignment to the SSCS and optionally a second TABULAR file as input.
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	9 # The program produces a plot which shows a histogram of Hamming distances separated after family sizes,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	10 # a family size distribution separated after Hamming distances for all (sample_size=0) or a given sample of SSCSs or SSCSs, which form a DCS.
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	11 # In additon, the tool produces HD and FSD plots for the difference between the HDs of both parts of the tags and for the chimeric reads
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	12 # and finally a CSV file with the data of the plots.
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	13 # It is also possible to perform the HD analysis with shortened tags with given sizes as input.
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 /
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	17 # --only_DCS True --FamilySize3 True --subset_tag True --nproc int --minFS int --maxFS int --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	18
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	19 import argparse
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	20 import itertools
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	21 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	22 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	23 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	24 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	25 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	26 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	27 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	28
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	29 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	30 import numpy
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	31 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	32
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	33 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	34
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	35
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	36 def plotFSDwithHD2(familySizeList1, maximumXFS, minimumXFS, originalCounts,
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	37 title_file1, subtitle, pdf, relative=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	38 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	39 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	40 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	41 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	42 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	43 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	44 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	45 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	46 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	47
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	48 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	49 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	50 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	51 p1 = numpy.bincount(numpy.concatenate((familySizeList1)))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	52 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	53
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	54 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	55 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	56 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	57 range1 = range(0, maximumXFS + 2)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	58 counts = plt.hist(familySizeList1, label=labels,
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	59 color=colors, stacked=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	60 rwidth=0.8, alpha=1, align="left",
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	61 edgecolor="None", bins=range1)
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	62 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	63
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	64 # plt.title(title_file1, fontsize=12)
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	65 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	66 plt.xlabel("Family size", fontsize=14)
316fbf91dd12 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit f9d5547849dabb59a33a5e998bda4730323d62a9 mheinzl parents: 1 diff changeset	67 plt.ylabel("Absolute Frequency", fontsize=14)
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	68
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	69 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	70 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	71 if maximumXFS >= 20:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	72 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	73 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	74 [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	75
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	76 plt.xlim((0, maximumXFS + 1))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	77 if len(numpy.concatenate(familySizeList1)) != 0:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	78 plt.ylim((0, max(numpy.bincount(numpy.concatenate(familySizeList1))) * 1.1))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	79
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	80 plt.ylim((0, maximumY * 1.2))
21 9919024d7778 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6 mheinzl parents: 20 diff changeset	81 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	82 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	83
11 7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9 mheinzl parents: 10 diff changeset	84 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	85 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	86 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	87 else:
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 = max(originalCounts)
9919024d7778 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6 mheinzl parents: 20 diff changeset	89 legend1 = "{}\n{}\n{:.5f}".format(max_count, count[len(count) - 1], float(count[len(count) - 1]) / sum(count))
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	90 plt.text(0.5, -0.08, legend1, size=12, transform=plt.gcf().transFigure)
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	91 legend3 = "singletons\n{:,}\n{:.5f}".format(int(counts[0][len(counts[0]) - 1][1]), float(counts[0][len(counts[0]) - 1][1]) / sum(counts[0][len(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	92 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	93 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	94
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	95 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	96 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	97
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	98
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	99 def plotHDwithFSD(list1, maximumX, minimumX, subtitle, lenTags, title_file1, pdf, xlabel, relative=False, nr_above_bars=True, nr_unique_chimeras=0, len_sample=0):
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	100 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	101 step = 0.1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	102 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	103 step = 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	104
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	105 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	106 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	107 con_list1 = numpy.concatenate(list1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	108 p1 = numpy.array([v for k, v in sorted(Counter(con_list1).iteritems())])
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	109 maximumY = numpy.amax(p1)
28 1fa7342a140d planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 27 diff changeset	110 maximumX = int(maximumX)
1fa7342a140d planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 27 diff changeset	111 print("max X", maximumX )
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	112
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	113 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	114 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	115 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	116 bin1 = maximumX + 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	117
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	118 counts = plt.hist(list1, bins=bin1, edgecolor='black', linewidth=1,
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	119 label=["FS=1", "FS=2", "FS=3", "FS=4", "FS=5-10",
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	120 "FS>10"], rwidth=0.8,
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	121 color=["#808080", "#FFFFCC", "#FFBF00", "#DF0101", "#0431B4", "#86B404"],
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	122 stacked=True, alpha=1,
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	123 align="left",
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	124 range=(0, maximumX + 1))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	125 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	126 bins = counts[1] # width of bins
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	127 counts = numpy.array(map(int, counts[0][5]))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	128 plt.suptitle(subtitle, y=1, x=0.5, 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	129 # plt.title(title_file1, fontsize=12)
2 316fbf91dd12 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit f9d5547849dabb59a33a5e998bda4730323d62a9 mheinzl parents: 1 diff changeset	130 plt.xlabel(xlabel, fontsize=14)
316fbf91dd12 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit f9d5547849dabb59a33a5e998bda4730323d62a9 mheinzl parents: 1 diff changeset	131 plt.ylabel("Absolute Frequency", fontsize=14)
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	132
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	133 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	134 plt.axis((minimumX - step, maximumX + step, 0, numpy.amax(counts) + sum(counts) * 0.1))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	135 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	136
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	137 plt.ylim((0, maximumY * 1.2))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	138
14 883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e mheinzl parents: 13 diff changeset	139 if nr_above_bars is True:
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e mheinzl parents: 13 diff changeset	140 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	141 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	142 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	143 continue
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e mheinzl parents: 13 diff changeset	144 else:
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e mheinzl parents: 13 diff changeset	145 plt.annotate("{:,}\n{:.3f}".format(x_label, float(x_label) / sum(counts), 1),
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e mheinzl parents: 13 diff changeset	146 xy=(label, x_label + len(con_list1) * 0.01),
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	147 xycoords="data", color="#000066", fontsize=10)
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	148
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	149 legend = "nr. of tags = {:,}\nsample size = {:,}\nnr. of data points = {:,}".format(lenTags, len_sample, sum(counts))
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	150 plt.text(0.14, -0.05, legend, size=12, transform=plt.gcf().transFigure)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	151
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	152 # if nr_unique_chimeras != 0 and len_sample != 0:
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	153 # if relative == True:
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	154 # legend = "nr. of unique chimeric tags= {:,} ({:.5f}) (rel.diff=1)".format(nr_unique_chimeras,
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	155 # int(nr_unique_chimeras) / float(len_sample))
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	156 # else:
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	157 # legend = "nr. of unique chimeric tags= {:,} ({:.5f})".format(nr_unique_chimeras, int(nr_unique_chimeras) / float(len_sample))
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	158 # plt.text(0.14, -0.09, 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	159
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	160 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	161 plt.close("all")
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	162 plt.clf()
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	163
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	164
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	165 def plotHDwithinSeq_Sum2(sum1, sum1min, sum2, sum2min, min_value, lenTags, title_file1, pdf, len_sample):
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	166 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	167 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	168
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	169 ham_partial = [sum1, sum1min, sum2, sum2min, numpy.array(min_value)] # new hd within tags
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	170
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	171 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	172 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	173 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	174
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	175 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	176 range1 = minimumX
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	177 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	178 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	179
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	180 plt.hist(ham_partial, align="left", rwidth=0.8, stacked=False, label=["HD a", "HD b'", "HD b", "HD a'", "HD a+b"], bins=range1, color=["#58ACFA", "#0404B4", "#FE642E", "#B40431", "#585858"], edgecolor='black', linewidth=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	181
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	182 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	183 plt.suptitle('Hamming distances within tags', 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	184 # plt.title(title_file1, fontsize=12)
14 883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e mheinzl parents: 13 diff changeset	185 plt.xlabel("HD", fontsize=14)
2 316fbf91dd12 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit f9d5547849dabb59a33a5e998bda4730323d62a9 mheinzl parents: 1 diff changeset	186 plt.ylabel("Absolute Frequency", fontsize=14)
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	187 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	188
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	189 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	190 plt.xticks(numpy.arange(0, maximumX + 1, 1.0))
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	191 # plt.ylim(0, maximumY * 1.2)
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	192 legend = "nr. of tags = {:,}\nsample size = {:,}\nnr. of data points = {:,}".format(lenTags, len_sample, len(numpy.concatenate(ham_partial)))
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	193
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	194 # legend = "sample size= {:,} against {:,}".format(len(numpy.concatenate(ham_partial)), lenTags)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	195 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	196 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	197 plt.close("all")
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	198 plt.clf()
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	199
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	200
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	201 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	202 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	203 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	204 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	205 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	206 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	207 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	208 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	209
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	210 state = 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	211 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	212 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	213 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	214 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	215 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	216 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	217 state = state + 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	218 continue
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	219 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	220 if state == 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	221 for i, 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	222 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	223 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	224 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	225 if state == 2:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	226 for i, l in zip(uniqueFS, nr):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	227 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	228 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	229 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	230
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	231 if state == 3:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	232 for i, l in zip(uniqueFS, nr):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	233 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	234 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	235 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	236
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	237 if state == 4:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	238 for i, l in zip(uniqueFS, nr):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	239 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	240 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	241 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	242
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	243 if state == 5:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	244 for i, l in zip(uniqueFS, nr):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	245 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	246 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	247 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	248
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	249 if state == 6:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	250 for i, l in zip(uniqueFS, nr):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	251 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	252 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	253 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	254
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	255 if state == 7:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	256 for i, l in zip(uniqueFS, nr):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	257 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	258 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	259 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	260 state = state + 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	261
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	262 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	263 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	264
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	265 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	266 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	267 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	268
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	269 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	270 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	271
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	272 return (final, sumCol)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	273
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	274
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	275 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	276 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	277 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	278 if diff is False:
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 output_file.write("{}HD=1{}HD=2{}HD=3{}HD=4{}HD=5-8{}HD>8{}sum{}\n".format(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	280 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	281 if rel is False:
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	282 output_file.write("{}diff=0{}diff=1{}diff=2{}diff=3{}diff=4{}diff=5-8{}diff>8{}sum{}\n".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	283 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	284 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".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	285
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	286 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	287 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	288 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	289 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	290 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	291 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	292 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	293 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	294 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	295 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	296 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	297 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	298 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	299
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	300
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	301 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	302 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	303 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	304 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	305 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	306 state = 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	307 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	308 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	309 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	310 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	311 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	312 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	313 state = state + 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	314 continue
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	315 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	316 if state == 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	317 for i, 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	318 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	319 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	320 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	321 if state == 2:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	322 for i, l in zip(uniqueHD, nr):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	323 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	324 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	325 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	326
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	327 if state == 3:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	328 for i, l in zip(uniqueHD, nr):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	329 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	330 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	331 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	332
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	333 if state == 4:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	334 for i, l in zip(uniqueHD, nr):
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] == uniqueHD[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, 3] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	338
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	339 if state == 5:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	340 for i, l in zip(uniqueHD, nr):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	341 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	342 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	343 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	344
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	345 if state == 6:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	346 for i, l in zip(uniqueHD, nr):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	347 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	348 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	349 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	350 state = state + 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	351
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	352 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	353 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	354 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	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
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	357 return (final, sumCol)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	358
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	359
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	360 def createTableHDwithTags(list1):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	361 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	362 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	363 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	364 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	365
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	366 state = 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	367 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	368 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	369 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	370 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	371 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	372 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	373 state = state + 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	374 continue
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	375 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	376 if state == 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	377 for i, 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	378 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	379 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	380 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	381 if state == 2:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	382 for i, l in zip(uniqueHD, nr):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	383 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	384 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	385 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	386 if state == 3:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	387 for i, l in zip(uniqueHD, nr):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	388 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	389 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	390 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	391 if state == 4:
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	392 for i, l in zip(uniqueHD, nr):
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	393 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	394 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	395 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	396 if state == 5:
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	397 for i, l in zip(uniqueHD, nr):
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	398 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	399 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	400 count[l, 4] = 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	401
1 7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	402 state = state + 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	403
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	404 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	405 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	406 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	407 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	408
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	409 return (final, sumCol)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce mheinzl parents: 0 diff changeset	410
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	411
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	412 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	413 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	414 output_file.write("\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	415 output_file.write("{}FS=1{}FS=2{}FS=3{}FS=4{}FS=5-10{}FS>10{}sum{}\n".format(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	416 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	417 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	418 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	419 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	420 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	421 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	422 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	423 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	424 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	425 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	426 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	427 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	428 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	429
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	430
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	431 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	432 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	433 output_file.write("\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	434 output_file.write("{}HD a{}HD b'{}HD b{}HD a'{}HD 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	435 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	436 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	437 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	438 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	439 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	440 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	441 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	442 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	443 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	444 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	445 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	446 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	447 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	448
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	449
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	450 def hamming(array1, array2):
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	451 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	452 i = 0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	453 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	454 for a in array1:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	455 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	456 res[i] = numpy.amin(dist[dist > 0]) # pick min distance greater than zero
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	457 # print(i)
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	458 i += 1
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	459 return res
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	460
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	461
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	462 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	463 array2 = numpy.unique(array2) # remove duplicate sequences to decrease running time
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	464
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	465 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	466 array1_half2 = numpy.array([i[len(i) / 2:len(i)] for i in array1]) # mate1 part 2
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	467
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	468 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	469 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	470
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	471 # 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	472 # 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	473 # 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	474 # 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	475 # 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	476 # 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	477 # 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	478 # 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	479
8 e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a mheinzl parents: 7 diff changeset	480 diff11 = []
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a mheinzl parents: 7 diff changeset	481 relativeDiffList = []
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a mheinzl parents: 7 diff changeset	482 ham1 = []
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a mheinzl parents: 7 diff changeset	483 ham2 = []
14 883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e mheinzl parents: 13 diff changeset	484 ham1min = []
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e mheinzl parents: 13 diff changeset	485 ham2min = []
8 e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a mheinzl parents: 7 diff changeset	486 min_valueList = []
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a mheinzl parents: 7 diff changeset	487 min_tagsList = []
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a mheinzl parents: 7 diff changeset	488 diff11_zeros = []
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a mheinzl parents: 7 diff changeset	489 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	490 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	491 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	492 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	493 half1_mate1 = array1_half
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	494 half2_mate1 = array1_half2
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	495 half1_mate2 = array2_half
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	496 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	497 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	498 half1_mate1 = array1_half2
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	499 half2_mate1 = array1_half
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	500 half1_mate2 = array2_half2
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	501 half2_mate2 = array2_half
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	502 # 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	503 # 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	504 # 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	505 # 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	506
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	507 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	508 # 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	509 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	510 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	511 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	512
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	513 # 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	514 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	515 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	516 array2_withoutSame = array2[index_withoutSame] # whole tag (=not splitted into 2 halfs)
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	517
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	518 dist = numpy.array([sum(itertools.imap(operator.ne, a, c)) for c in
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	519 array2_half_withoutSame]) # calculate HD of "a" in the tag to all "a's" or "b" in the tag to all "b's"
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	520 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	521 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	522 # min_value = dist[min_index] # get minimum HDs
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	523 min_tag_half2 = array2_half2_withoutSame[min_index] # get all "b's" of the tag or all "a's" of the tag with minimum HD
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	524 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	525
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	526 dist_second_half = numpy.array([sum(itertools.imap(operator.ne, b, e)) for e in min_tag_half2]) # calculate HD of "b" to all "b's" or "a" to all "a's"
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	527 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	528 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	529 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	530
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	531 # 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	532 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	533 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	534 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	535 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	536 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	537 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	538
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	539 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	540 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	541 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	542 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	543 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	544 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	545
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	546 # 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	547 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	548 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	549 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	550 diff11_zeros.append(difference1_zeros)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	551 max_tag_list.append(max_tag)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	552 else:
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	553 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	554 diff11_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	555 max_tag_list.append(numpy.array(["None"]))
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	556
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	557 # max_tag_list.append(numpy.array(max_tag))
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	558
8 e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a mheinzl parents: 7 diff changeset	559 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	560
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	561 # 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	562 # 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	563 # 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	564 # 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	565 # 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	566 # 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	567 # 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	568 # 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	569 # min_tagsList_zeros = [st for st in min_tagsList_zeros if st != 999]
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	570 return ([diff11, ham1, ham2, min_valueList, min_tagsList, relativeDiffList, diff11_zeros, 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	571
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	572
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	573 def readFileReferenceFree(file):
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	574 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	575 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	576 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	577 return(integers, data_array)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	578
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
11 7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9 mheinzl parents: 10 diff changeset	580 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	581 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	582 maximum = max(ham)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	583 minimum = min(ham)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	584 ham = numpy.asarray(ham)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	585
11 7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9 mheinzl parents: 10 diff changeset	586 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	587 data = ham[singletons]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	588
11 7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9 mheinzl parents: 10 diff changeset	589 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	590 data2 = ham[hd2]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	591
11 7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9 mheinzl parents: 10 diff changeset	592 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	593 data3 = ham[hd3]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	594
11 7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9 mheinzl parents: 10 diff changeset	595 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	596 data4 = ham[hd4]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	597
11 7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9 mheinzl parents: 10 diff changeset	598 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	599 data5 = ham[hd5]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	600
11 7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9 mheinzl parents: 10 diff changeset	601 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	602 data6 = ham[hd6]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	603
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	604 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	605 return(list1, maximum, minimum)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	606
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	607
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	608 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	609 hammingDistances = numpy.unique(ham)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	610 fs = numpy.asarray(fs)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	611
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	612 ham = numpy.asarray(ham)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	613 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	614 if len(bigFamilies2) != 0:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	615 fs[bigFamilies2] = 20
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	616 maximum = max(fs)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	617 minimum = min(fs)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	618 if diff is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	619 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	620 data0 = fs[hd0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	621
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	622 if rel is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	623 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	624 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	625 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	626 data = fs[hd1]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	627
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	628 if rel is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	629 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	630 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	631 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	632 data2 = fs[hd2]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	633
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	634 if rel is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	635 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	636 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	637 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	638 data3 = fs[hd3]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	639
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	640 if rel is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	641 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	642 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	643 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	644 data4 = fs[hd4]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	645
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	646 if rel is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	647 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	648 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	649 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	650 data5 = fs[hd5]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	651
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	652 if rel is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	653 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	654 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	655 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	656 data6 = fs[hd6]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	657
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	658 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	659 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	660 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	661 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	662
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	663 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	664
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	665
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	666 def make_argparser():
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	667 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	668 parser.add_argument('--inputFile',
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	669 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	670 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	671 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	672 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	673 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	674 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	675 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	676 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	677 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	678 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	679
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	680 parser.add_argument('--minFS', default=1, type=int,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	681 help='Only tags, which have a family size greater or equal than specified, 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	682 parser.add_argument('--maxFS', default=0, type=int,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	683 help='Only tags, which have a family size smaller or equal than specified, 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	684 parser.add_argument('--nr_above_bars', action="store_true",
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	685 help='If no, values above bars in the histograms are removed')
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	686
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	687 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	688 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	689 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	690 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	691 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	692 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	693
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	694 return parser
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	695
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	696
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	697 def Hamming_Distance_Analysis(argv):
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	698
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	699 parser = make_argparser()
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	700 args = parser.parse_args(argv[1:])
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	701
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	702 file1 = args.inputFile
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	703 name1 = args.inputName1
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 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 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	706 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	707 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	708 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	709
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	710 sep = "\t"
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	711 onlyDuplicates = args.only_DCS
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	712 minFS = args.minFS
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	713 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	714 nr_above_bars = args.nr_above_bars
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	715
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	716 subset = args.subset_tag
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	717 nproc = args.nproc
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	718
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	719 # input checks
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	720 if index_size < 0:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	721 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	722 exit(2)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	723
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	724 if nproc <= 0:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	725 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	726 exit(3)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	727
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	728 if subset < 0:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	729 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	730 exit(5)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	731
19 2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty mheinzl parents: 18 diff changeset	732 # PLOT
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	733 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	734 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	735 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	736 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	737 plt.rc('figure', figsize=(11.69, 8.27)) # A4 format
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	738
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	739 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	740
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	741 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	742 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	743 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	744 data_array = numpy.array(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	745 print("total nr of tags with Ns:", 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	746 n = [i for i, x in enumerate(data_array[:, 1]) if "N" in x]
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	747 if len(n) != 0: # delete tags with N in the tag from data
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	748 print("nr of tags with N's within tag:", len(n), float(len(n)) / len(data_array))
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	749 index_whole_array = numpy.arange(0, len(data_array), 1)
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	750 index_withoutN_inTag = numpy.delete(index_whole_array, n)
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	751 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	752 integers = integers[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	753 print("total nr of tags without Ns:", len(data_array))
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	754
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	755 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	756 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	757 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	758
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	759 # 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	760 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	761 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	762 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	763 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	764
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	765 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	766 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	767 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	768
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	769 # 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	770 u, index_unique, c = numpy.unique(numpy.array(seq), return_counts=True, return_index=True)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	771 d = u[c > 1]
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	772
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	773 # 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	774 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	775 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	776 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	777
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	778 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	779 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	780
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	781 if minFS > 1:
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	782 duplTags_tag = duplTags_tag[(duplTags >= 3) & (duplTagsBA >= 3)]
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	783 duplTags_seq = duplTags_seq[(duplTags >= 3) & (duplTagsBA >= 3)]
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	784 duplTags = duplTags[(duplTags >= 3) & (duplTagsBA >= 3)] # ab+ba with FS>=3
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	785
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	786 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	787 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	788 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	789 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	790
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	791 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	792 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	793
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	794 # 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	795 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	796 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	797 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	798
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	799 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	800 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	801 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	802 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	803 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	804 else:
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	805 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	806 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	807 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	808 [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	809 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	810 [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	811
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	812 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	813 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	814
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	815 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	816 # 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	817 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	818 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	819 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	820 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	821 unique_tags, unique_indices = numpy.unique(data_array[:, 1], return_index=True) # get only unique tags
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	822 result = numpy.random.choice(unique_indices, size=index_size, 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	823
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	824 # 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	825 # 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	826 # 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	827
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	828 # with open("index_result1_{}.pkl".format(app_f), "wb") as o:
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	829 # 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	830
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	831 # 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	832 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	833 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	834 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	835
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	836 # 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	837 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	838 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	839 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	840 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	841 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	842 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	843 # 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	844 # 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	845 # 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	846
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	847 # # 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	848 # 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	849
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	850 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	851 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	852 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	853 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	854 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	855 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	856 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	857 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	858 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	859 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	860 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	861 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	862 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	863 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	864 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	865
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	866 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	867 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	868 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	869 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	870
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	871 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	872 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	873 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	874 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	875 minHD_tags_zeros2 = numpy.concatenate([item[7] 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	876 chim_tags = [item[10] 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	877 chim_tags2 = [item[10] 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	878 chimera_tags1 = [ii if isinstance(i, list) else i for i in chim_tags for ii in i]
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	879 chimera_tags2 = [ii if isinstance(i, list) else i for i in chim_tags2 for ii in i]
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	880
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	881 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	882 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	883 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	884 diff = []
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	885 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	886 for d1, d2, rel1, rel2, zeros1, zeros2, tag1, tag2, ctag1, ctag2 in \
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	887 zip(diff1, diff2, rel_Diff1, rel_Diff2, diff_zeros1, diff_zeros2, minHD_tags_zeros1, minHD_tags_zeros2, chimera_tags1, chimera_tags2):
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	888 rel_Diff.append(max(rel1, rel2))
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	889 diff.append(max(d1, d2))
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
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	891 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	892 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	893 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	894 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	895 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	896 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	897 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	898 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	899 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	900 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	901 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	902 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	903 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	904
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	905 chimera_tags_new = 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	906 #data_chimeraAnalysis = numpy.column_stack((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	907 # 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	908 #
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	909 # 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	910 # 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	911 # 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	912 # 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	913
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	914 with open(output_chimeras_tabular, "w") as output_file1:
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	915 output_file1.write("chimera tag\tsimilar tag with HD=0\n")
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	916 for i in range(len(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	917 tag1 = minHD_tags_zeros[i]
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	918 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	919 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	920
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	921 max_tags = chimera_tags_new[i]
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	922 if isinstance(max_tags, list) and len(max_tags) > 1:
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	923 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	924 #if isinstance(max_tags, list): #and type(max_tags) 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	925 # print(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	926 # 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	927 max_tags = numpy.unique(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	928
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	929 chimera_half_a = numpy.array([i[0:(len(i)) / 2] for i in max_tags]) # mate1 part1
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	930 chimera_half_b = numpy.array([i[len(i) / 2:len(i)] for i in max_tags]) # mate1 part 2
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	931
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	932 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	933 for j in range(len(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	934 if sample_half_a == chimera_half_a[j]:
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	935 max_tag = "{} {}".format(chimera_half_a[j], chimera_half_b[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	936 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	937
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	938 elif sample_half_b == chimera_half_b[j]:
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	939 max_tag = "{} {}".format(chimera_half_a[j], chimera_half_b[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	940 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	941
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	942 sample_tag = "{} {}".format(sample_half_a, sample_half_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	943 output_file1.write("{}\t{}\n".format(sample_tag, ", ".join(new_format)))
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	944 output_file1.write(
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	945 "This file contains all tags that were identified as chimeras as the first column and the corresponding tags which returned a Hamming distance of zero in either the first or the second half of the sample tag as the second column.\n "
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	946 "The tags were separated by an empty space into their halves and the * marks the identical half.")
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	947
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	948 # unique_chimeras = numpy.array(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	949 #
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	950 # sample_half_a = numpy.array([i[0:(len(i)) / 2] for i in unique_chimeras]) # mate1 part1
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	951 # sample_half_b = numpy.array([i[len(i) / 2:len(i)] for i in unique_chimeras]) # mate1 part 2
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	952 #
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	953 # output_file1.write("sample tag\tsimilar tag\n")
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	954 # for tag1, a, b in zip(unique_chimeras, sample_half_a, sample_half_b):
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	955 # max_tags = numpy.concatenate(chimeras_dic.get(tag1))
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	956 # max_tags = numpy.unique(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	957 #
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	958 # chimera_half_a = numpy.array([i[0:(len(i)) / 2] for i in max_tags]) # mate1 part1
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	959 # chimera_half_b = numpy.array([i[len(i) / 2:len(i)] for i in max_tags]) # mate1 part 2
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	960 #
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	961 # new_format = []
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	962 # for i in range(len(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	963 # if a == chimera_half_a[i]:
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	964 # max_tag = "{} {}".format(chimera_half_a[i], chimera_half_b[i])
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	965 # new_format.append(max_tag)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	966 #
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	967 # elif b == chimera_half_b[i]:
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	968 # max_tag = "{} {}".format(chimera_half_a[i], chimera_half_b[i])
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	969 # new_format.append(max_tag)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	970 #
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	971 # sample_tag = "{} {}".format(a, b)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	972 # output_file1.write("{}\t{}\n".format(sample_tag, ", ".join(new_format)))
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	973 # output_file1.write(
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	974 # "This file contains all tags that were identified as chimeras as the first column and the corresponding tags which returned a Hamming distance of zero in either the first or the second half of the sample tag as the second column.\n "
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	975 # "The tags were separated by an empty space into their halves and the * marks the identical half.")
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	976
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	977 nr_chimeric_tags = len(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	978 print("nr of unique chimeras", nr_chimeric_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	979
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	980 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	981 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	982
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	983 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	984 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	985 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	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 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	988 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	989 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	990 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	991 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	992 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	993 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	994
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	995 # 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	996 # 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	997 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	998 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	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 # 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	1001 # 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	1002 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	1003 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	1004 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	1005 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	1006 else:
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1007 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	1008
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1009 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	1010 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	1011 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	1012
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1013 if onlyDuplicates:
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1014 lst_minHD_tags = numpy.concatenate(([item[0] for item in lst_minHD_tags], [item_b[1] for item_b in lst_minHD_tags])).astype(int)
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1015
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1016 # 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	1017 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	1018 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	1019 rel_Diff)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1020 # 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	1021 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	1022 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	1023 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	1024 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	1025 if onlyDuplicates:
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1026 lst_minHD_tags_zeros = numpy.concatenate(([item[0] for item in lst_minHD_tags_zeros], [item_b[1] for item_b in lst_minHD_tags_zeros])).astype(int)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1027
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1028 # histogram with HD of non-identical half
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1029 listDifference1_zeros, maximumXDifference_zeros, minimumXDifference_zeros = hammingDistanceWithFS(lst_minHD_tags_zeros, 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	1030
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1031 # plot Hamming Distance with Family size distribution
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1032 plotHDwithFSD(list1=list1, maximumX=maximumX, minimumX=minimumX, pdf=pdf,
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1033 subtitle="Hamming distance separated by family size", title_file1=name1, 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	1034 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	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 # Plot FSD with separation after
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1037 plotFSDwithHD2(familySizeList1, maximumXFS, minimumXFS,
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1038 originalCounts=quant, subtitle="Family size distribution separated by Hamming distance",
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1039 pdf=pdf, relative=False, title_file1=name1, diff=False)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1040
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1041 # Plot 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	1042 plotHDwithinSeq_Sum2(HDhalf1, HDhalf1min, HDhalf2, HDhalf2min, minHDs, pdf=pdf, 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	1043 title_file1=name1, 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	1044
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1045 # 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	1046 plotHDwithFSD(listDifference1, maximumXDifference, minimumXDifference, pdf=pdf,
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1047 subtitle="Delta Hamming distance within tags",
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1048 title_file1=name1, 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	1049 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	1050
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1051 plotHDwithFSD(listRelDifference1, maximumXRelDifference, minimumXRelDifference, pdf=pdf,
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1052 subtitle="Chimera Analysis: relative delta Hamming distances",
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1053 title_file1=name1, lenTags=lenTags,
22 7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 21 diff changeset	1054 xlabel="relative delta HD", relative=True, nr_above_bars=nr_above_bars, 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	1055
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1056 # 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	1057 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	1058 # 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	1059 plotHDwithFSD(listDifference1_zeros, maximumXDifference_zeros, minimumXDifference_zeros, pdf=pdf, subtitle="Hamming distance of chimeras",
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1060 title_file1=name1, 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	1061 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	1062
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1063 # 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	1064 # HD
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1065 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	1066 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	1067
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1068 # FSD
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1069 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	1070 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	1071
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1072 # 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	1073 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	1074 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	1075
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1076 # HD
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1077 # absolute difference
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1078 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	1079 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	1080 # 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	1081 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	1082 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	1083
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1084 # chimeric reads
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1085 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	1086 # 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	1087 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	1088 overallSum15 = sum(sumCol15)
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	1089
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1090 output_file.write("{}\n".format(name1))
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1091 output_file.write("number of tags per file{}{:,} (from {:,}) against {:,}\n\n".format(sep, len(
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1092 numpy.concatenate(list1)), lenTags, lenTags))
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1093
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1094 # HD
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1095 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	1096 "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	1097 # FSD
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1098 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	1099 "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	1100 diff=False)
0 239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	1101
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1102 # 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	1103 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	1104 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	1105 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	1106 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	1107 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	1108 "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	1109
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1110 # 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	1111 output_file.write(
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1112 "The Hamming distances were calculated by comparing the first halve against all halves and selected the minimum value (HD a).\n"
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1113 "For the second half of the tag, we compared them against all tags which resulted in the minimum HD of the previous step and selected the maximum value (HD b').\n"
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1114 "Finally, it was possible to calculate the absolute and relative differences between the HDs (absolute and relative delta HD).\n"
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1115 "These calculations were repeated, but starting with the second half in the first step to find all possible chimeras in the data (HD b and HD For simplicity we used the maximum value between the delta values in the end.\n"
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1116 "When only tags that can form DCS were allowed in the analysis, family sizes for the 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	1117
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1118 output_file.write("length of one part of the tag = {}\n\n".format(len(data_array[0, 1]) / 2))
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1119
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1120 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	1121 "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	1122 createFileHD(summary11, sumCol11, overallSum11, output_file,
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1123 "Absolute delta Hamming distances 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	1124
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1125 createFileHD(summary13, sumCol13, overallSum13, output_file,
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1126 "Chimera analysis: relative delta Hamming distances", sep)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1127
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1128 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	1129 output_file.write(
25 9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 22 diff changeset	1130 "Chimeras:\nAll tags were filtered: only those tags where at least one half was identical (HD=0) and therefore, had a relative delta of 1 were kept. These tags are considered as chimeric.\nSo the Hamming distances 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	1131 createFileHD(summary15, sumCol15, overallSum15, output_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	1132 "Hamming distances of chimeras", 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	1133
20 b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025 mheinzl parents: 19 diff changeset	1134 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	1135
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	1136
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	1137 if __name__ == '__main__':
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a mheinzl parents: diff changeset	1138 sys.exit(Hamming_Distance_Analysis(sys.argv))

Mercurial > repos > mheinzl > hd

annotate hd.py @ 28:1fa7342a140d draft