Mercurial > repos > mheinzl > hd

annotate hd.py @ 21:9919024d7778 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6
author mheinzl
date Fri, 14 Dec 2018 05:03:24 -0500
parents b084b6a8e3ac
children 7e570ba56b83
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
16 # USAGE: python hd.py --inputFile filename --inputName1 filename --sample_size int/0 --sep "characterWhichSeparatesCSVFile" /
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
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
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
23 from collections import Counter
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
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
26
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
27 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
28 import numpy
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
29 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
30
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
31 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
32
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
33
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
34 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
35 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
36 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
37 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
38 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
39 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
40 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
41 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
42 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
43 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
44 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
45
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
46 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
47 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
48 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
49 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
50 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
51
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
52 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
53 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
54 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
55 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
56 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
57 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
58 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
59 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
60 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
61
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
62 # 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
63 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
64 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
65 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
66
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
67 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
68 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
69 if maximumXFS >= 20:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
70 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
71 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
72 [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
73
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
74 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
75 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
76 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
77
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, 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
79 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
80 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
81
11
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
mheinzl
parents: 10
diff changeset
82 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
83 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
84 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
85 else:
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 = max(originalCounts)
9919024d7778 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6
mheinzl
parents: 20
diff changeset
87 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
88 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
89 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
90 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
91 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
92
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
93 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
94 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
95
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
96
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
97 def plotHDwithFSD(list1, maximumX, minimumX, subtitle, lenTags, title_file1, pdf, xlabel, relative=False, nr_above_bars=True):
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
98 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
99 step = 0.1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
100 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
101 step = 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
102
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
103 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
104 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
105 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
106 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
107 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
108
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
109 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
110 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
111 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
112 bin1 = maximumX + 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
113
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
114 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
115 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
116 "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
117 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
118 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
119 align="left",
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
120 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
121 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
122 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
123 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
124 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
125 # 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
126 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
127 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
128
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
129 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
130 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
131 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
132
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
133 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
134
14
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
135 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
136 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
137 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
138 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
139 continue
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
140 else:
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
141 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
142 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
143 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
144
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
145 legend = "sample size= {:,} against {:,}".format(sum(counts), lenTags)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
146 plt.text(0.14, -0.01, 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
147
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
148 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
149 plt.close("all")
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
150 plt.clf()
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
151
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
152
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
153 def plotHDwithinSeq_Sum2(sum1, sum1min, sum2, sum2min, min_value, lenTags, title_file1, pdf):
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
154 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
155 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
156
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
157 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
158
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
159 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
160 minimumX = numpy.amin(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
161 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
162
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
163 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
164 range1 = minimumX
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
165 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
166 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
167
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
168 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)
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
169
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
170 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
171 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
172 # 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
173 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
174 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
175 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
176
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
177 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
178 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
179 # plt.ylim(0, maximumY * 1.2)
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
180
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
181 legend = "sample size= {:,} against {:,}".format(len(numpy.concatenate(ham_partial)), lenTags)
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
182 plt.text(0.14, -0.01, 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
183 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
184 plt.close("all")
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
185 plt.clf()
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
186
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
187
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
188 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
189 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
190 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
191 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
192 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
193 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
194 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
195 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
196
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
197 state = 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
198 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
199 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
200 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
201 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
202 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
203 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
204 state = state + 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
205 continue
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
206 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
207 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
208 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
209 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
210 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
211 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
212 if state == 2:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
213 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
214 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
215 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
216 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
217
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
218 if state == 3:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
219 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
220 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
221 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
222 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
223
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
224 if state == 4:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
225 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
226 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
227 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
228 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
229
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
230 if state == 5:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
231 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
232 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
233 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
234 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
235
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
236 if state == 6:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
237 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
238 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
239 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
240 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
241
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
242 if state == 7:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
243 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
244 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
245 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
246 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
247 state = state + 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 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
250 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
251
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
252 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
253 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
254 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
255
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
256 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
257 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
258
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
259 return (final, sumCol)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
260
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
261
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
262 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
263 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
264 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
265 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
266 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
267 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
268 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
269 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
270 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
271 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
272
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
273 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
274 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
275 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
276 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
277 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
278 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
279 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
280 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
281 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
282 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
283 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
284 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
285 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
286
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
287
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
288 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
289 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
290 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
291 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
292 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
293 state = 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
294 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
295 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
296 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
297 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
298 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
299 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
300 state = state + 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
301 continue
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
302 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
303 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
304 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
305 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
306 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
307 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
308 if state == 2:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
309 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
310 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
311 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
312 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
313
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
314 if state == 3:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
315 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
316 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
317 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
318 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
319
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
320 if state == 4:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
321 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
322 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
323 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
324 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
325
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
326 if state == 5:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
327 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
328 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
329 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
330 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
331
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
332 if state == 6:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
333 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
334 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
335 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
336 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
337 state = state + 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 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
340 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
341 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
342 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
343
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
344 return (final, sumCol)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
345
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
346
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
347 def createTableHDwithTags(list1):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
348 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
349 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
350 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
351 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
352
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
353 state = 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
354 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
355 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
356 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
357 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
358 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
359 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
360 state = state + 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
361 continue
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
362 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
363 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
364 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
365 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
366 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
367 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
368 if state == 2:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
369 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
370 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
371 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
372 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
373 if state == 3:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
374 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
375 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
376 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
377 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
378 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
379 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
380 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
381 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
382 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
383 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
384 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
385 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
386 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
387 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
388
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
389 state = state + 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
390
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
391 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
392 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
393 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
394 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
395
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
396 return (final, sumCol)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
397
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
398
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
399 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
400 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
401 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
402 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
403 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
404 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
405 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
406 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
407 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
408 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
409 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
410 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
411 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
412 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
413 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
414 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
415 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
416
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
417
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
418 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
419 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
420 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
421 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
422 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
423 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
424 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
425 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
426 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
427 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
428 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
429 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
430 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
431 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
432 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
433 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
434 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
435
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
436
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
437 def hamming(array1, array2):
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
438 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
439 i = 0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
440 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
441 for a in array1:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
442 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
443 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
444 # print(i)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
445 i += 1
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
446 return res
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
447
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
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
449 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
450 array2 = numpy.unique(array2) # remove duplicate sequences to decrease running time
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
451 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
452 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
453
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
454 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
455 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
456
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 # 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
458 # 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
459 # 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
460 # 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
461 # 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
462 # 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
463 # 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
464 # 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
465
8
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
466 diff11 = []
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
467 relativeDiffList = []
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
468 ham1 = []
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
469 ham2 = []
14
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
470 ham1min = []
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
471 ham2min = []
8
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
472 min_valueList = []
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
473 min_tagsList = []
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
474 diff11_zeros = []
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
475 min_tagsList_zeros = []
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
476 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
477 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
478 half1_mate1 = array1_half
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
479 half2_mate1 = array1_half2
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
480 half1_mate2 = array2_half
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
481 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
482 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
483 half1_mate1 = array1_half2
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
484 half2_mate1 = array1_half
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
485 half1_mate2 = array2_half2
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
486 half2_mate2 = array2_half
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
487
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
488 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
489 # exclude identical tag from array2, to prevent comparison to itself
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
490 sameTag = numpy.where(array2 == tag)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
491 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
492 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
493
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
494 # 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
495 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
496 array2_half2_withoutSame = half2_mate2[index_withoutSame]
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 # 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
498
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
499 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
500 array2_half_withoutSame]) # calculate HD of "a" in the tag to all "a's" or "b" in the tag to all "b's"
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
501 min_index = numpy.where(dist == dist.min()) # get index of min HD
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
502 min_value = dist[min_index] # get minimum HDs
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
503 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
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
504 # min_tag = 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
505
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
506 dist2 = numpy.array([sum(itertools.imap(operator.ne, b, e)) for e in
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
507 min_tag_half2]) # calculate HD of "b" to all "b's" or "a" to all "a's"
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 for d, d2 in zip(min_value, dist2):
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
509 if mate_b is True: # half2, corrects the variable of the HD from both halfs if it is a or b
14
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
510 ham2.append(d)
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
511 ham2min.append(d2)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
512 else: # half1, corrects the variable of the HD from both halfs if it is a or b
14
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
513 ham1.append(d)
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
514 ham1min.append(d2)
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
515
8
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
516 min_valueList.append(d + d2)
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
517 min_tagsList.append(tag)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
518 difference1 = abs(d - d2)
8
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
519 diff11.append(difference1)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
520 rel_difference = round(float(difference1) / (d + d2), 1)
8
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
521 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
522
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
523 # tags which have identical parts:
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
524 if d == 0 or d2 == 0:
8
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
525 min_tagsList_zeros.append(tag)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
526 difference1_zeros = abs(d - d2)
8
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
527 diff11_zeros.append(difference1_zeros)
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
528 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
529
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
530 # 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
531 # 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
532 # 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
533 # 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
534 # 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
535 # 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
536 # 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
537 # 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
538 # min_tagsList_zeros = [st for st in min_tagsList_zeros if st != 999]
2
316fbf91dd12 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit f9d5547849dabb59a33a5e998bda4730323d62a9
mheinzl
parents: 1
diff changeset
539
14
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
540 return ([diff11, ham1, ham2, min_valueList, min_tagsList, relativeDiffList, diff11_zeros, min_tagsList_zeros, ham1min, ham2min])
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
541
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
542
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
543 def readFileReferenceFree(file):
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
544 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
545 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
546 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
547 return(integers, data_array)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
548
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
549
11
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
mheinzl
parents: 10
diff changeset
550 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
551 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
552 maximum = max(ham)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
553 minimum = min(ham)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
554 ham = numpy.asarray(ham)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
555
11
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
mheinzl
parents: 10
diff changeset
556 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
557 data = ham[singletons]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
558
11
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
mheinzl
parents: 10
diff changeset
559 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
560 data2 = ham[hd2]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
561
11
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
mheinzl
parents: 10
diff changeset
562 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
563 data3 = ham[hd3]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
564
11
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
mheinzl
parents: 10
diff changeset
565 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
566 data4 = ham[hd4]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
567
11
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
mheinzl
parents: 10
diff changeset
568 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
569 data5 = ham[hd5]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
570
11
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
mheinzl
parents: 10
diff changeset
571 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
572 data6 = ham[hd6]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
573
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
574 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
575 return(list1, maximum, minimum)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
576
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
577
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
578 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
579 hammingDistances = numpy.unique(ham)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
580 fs = numpy.asarray(fs)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
581
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
582 ham = numpy.asarray(ham)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
583 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
584 if len(bigFamilies2) != 0:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
585 fs[bigFamilies2] = 20
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
586 maximum = max(fs)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
587 minimum = min(fs)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
588 if diff is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
589 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
590 data0 = fs[hd0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
591
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
592 if rel is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
593 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
594 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
595 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
596 data = fs[hd1]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
597
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
598 if rel is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
599 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
600 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
601 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
602 data2 = fs[hd2]
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 if rel is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
605 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
606 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
607 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
608 data3 = fs[hd3]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
609
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
610 if rel is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
611 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
612 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
613 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
614 data4 = fs[hd4]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
615
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
616 if rel is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
617 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
618 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
619 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
620 data5 = fs[hd5]
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 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
624 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
625 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
626 data6 = fs[hd6]
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 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
629 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
630 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
631 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
632
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
633 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
634
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
635
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
636 def make_argparser():
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
637 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
638 parser.add_argument('--inputFile',
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
639 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
640 parser.add_argument('--inputName1')
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
641 # parser.add_argument('--inputFile2', default=None,
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
642 # help='Tabular File with three columns: ab or ba, tag and family size.')
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
643 # parser.add_argument('--inputName2')
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
644 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
645 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
646 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
647 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
648 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
649 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
650 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
651 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
652
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
653 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
654 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
655 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
656 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
657 parser.add_argument('--nr_above_bars', action="store_true",
14
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
658 help='If no, values above bars in the histrograms 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
659
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
660 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
661 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
662 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
663 help='Name of the pdf file.')
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
664 # parser.add_argument('--output_pdf2', default="data2.pdf", type=str,
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
665 # help='Name of the pdf file.')
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
666 # parser.add_argument('--output_tabular2', default="data2.tabular", type=str,
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
667 # 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
668
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
669 return parser
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
670
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
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
672 def Hamming_Distance_Analysis(argv):
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
673 parser = make_argparser()
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
674 args = parser.parse_args(argv[1:])
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
675
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
676 file1 = args.inputFile
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
677 name1 = args.inputName1
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
678
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
679 # file2 = args.inputFile2
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
680 # name2 = args.inputName2
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
681
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
682 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
683 title_savedFile_pdf = args.output_pdf
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
684 # title_savedFile_pdf2 = args.output_pdf2
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
685
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 title_savedFile_csv = args.output_tabular
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
687 # title_savedFile_csv2 = args.output_tabular2
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
688
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
689 sep = "\t"
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
690 onlyDuplicates = args.only_DCS
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
691 minFS = args.minFS
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
692 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
693 nr_above_bars = args.nr_above_bars
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
694
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
695 subset = args.subset_tag
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
696 nproc = args.nproc
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
697
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
698 # input checks
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
699 if index_size < 0:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
700 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
701 exit(2)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
702
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
703 if nproc <= 0:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
704 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
705 exit(3)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
706
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
707 if subset < 0:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
708 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
709 exit(5)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
710
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
711 # PLOT
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
712 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
713 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
714 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
715 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
716 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
717
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
718 # if file2 != str(None):
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
719 # files = [file1, file2]
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
720 # name1 = name1.split(".tabular")[0]
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
721 # name2 = name2.split(".tabular")[0]
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
722 # names = [name1, name2]
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
723 # pdf_files = [title_savedFile_pdf, title_savedFile_pdf2]
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
724 # csv_files = [title_savedFile_csv, title_savedFile_csv2]
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
725 # else:
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
726 # f = file1
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
727 name1 = name1.split(".tabular")[0]
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
728 # name_file = name1
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
729 # pdf_f = title_savedFile_pdf
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
730 # csv_f = title_savedFile_csv
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
731
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
732 #for f, name_file, pdf_f, csv_f in zip(files, names, pdf_files, csv_files):
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
733 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
734 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
735 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
736 data_array = numpy.array(data_array)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
737 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
738 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
739 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
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 # 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
742 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
743 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
744 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
745 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
746
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
747 print("min FS", min(integers))
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
748 print("max FS", max(integers))
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
749
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
750 tags = data_array[:, 2]
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
751 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
752
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
753 if onlyDuplicates is True:
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
754 # 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
755 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
756 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
757
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
758 # 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
759 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
760 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
761 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
762
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
763 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
764 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
765
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
766 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
767 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
768 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
769 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
770
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
771 # 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
772 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
773 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
774 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
775
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
776 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
777 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
778 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
779 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
780 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
781 else:
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
782 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
783 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
784 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
785 [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
786 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
787 [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
788
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
789 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
790 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
791
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
792 print("length of tag= ", len(data_array[0, 1]))
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
793 # 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
794 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
795 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
796 else:
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
797 result = numpy.random.choice(len(integers), size=index_size,
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
798 replace=False) # array of random sequences of size=index.size
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
799
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
800 # 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
801 # 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
802
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
803 # 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
804 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
805 result2 = data_array[:, 1] # all tags
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
806 print("size of the whole dataset= ", len(result2))
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
807 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
808
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
809 # 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
810 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
811 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
812 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
813 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
814 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
815 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
816 # 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
817 # 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
818 # 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
819
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
820 # HD analysis 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
821 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
822 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
823 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
824 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
825 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
826 diff = numpy.concatenate((numpy.concatenate([item[0] 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
827 numpy.concatenate([item_b[0] 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
828 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
829 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
830 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
831 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
832 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
833 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
834 minHD_tags = numpy.concatenate((numpy.concatenate([item[4] 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
835 numpy.concatenate([item_b[4] for item_b in diff_list_b])))
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
836 rel_Diff = numpy.concatenate((numpy.concatenate([item[5] 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
837 numpy.concatenate([item_b[5] for item_b in diff_list_b])))
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
838 diff_zeros = numpy.concatenate((numpy.concatenate([item[6] 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
839 numpy.concatenate([item_b[6] 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
840 minHD_tags_zeros = numpy.concatenate((numpy.concatenate([item[7] 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
841 numpy.concatenate([item_b[7] for item_b in diff_list_b])))
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
842 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
843 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
844 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
845 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
846
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
847 lenTags = len(data_array)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
848
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
849 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
850 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
851 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
852
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
853 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
854 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
855 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
856 ham = numpy.tile(ham, 2)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
857
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
858 # 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
859 # 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
860 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
861 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
862
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
863 # 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
864 # there are more tags than sample size in the plot, because one tag can have multiple minimas
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
865 seqDic = dict(zip(seq, quant))
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
866 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
867 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
868 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
869
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
870 # 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
871 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
872 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
873 rel_Diff)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
874
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
875 # family size distribution separated after the 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
876 familySizeList1_diff, hammingDistances_diff, maximumXFS_diff, minimumXFS_diff = familySizeDistributionWithHD(
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
877 lst_minHD_tags, diff, diff=True, rel=False)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
878 familySizeList1_reldiff, hammingDistances_reldiff, maximumXFS_reldiff, minimumXFS_reldiff = familySizeDistributionWithHD(
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
879 lst_minHD_tags, rel_Diff, diff=True, rel=True)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
880
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
881 # 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
882 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
883 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
884 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
885 lst_minHD_tags_zeros.append(seqDic.get(i)) # get family size for tags of chimeric reads
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
886
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
887 # histogram with HD of non-identical half
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
888 listDifference1_zeros, maximumXDifference_zeros, minimumXDifference_zeros = hammingDistanceWithFS(
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
889 lst_minHD_tags_zeros, diff_zeros)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
890 # family size distribution of non-identical half
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
891 familySizeList1_diff_zeros, hammingDistances_diff_zeros, maximumXFS_diff_zeros, minimumXFS_diff_zeros = familySizeDistributionWithHD(
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
892 lst_minHD_tags_zeros, diff_zeros, diff=False, rel=False)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
893
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
894 # 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
895 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
896 subtitle="Hamming distance separated by family size", title_file1=name1, lenTags=lenTags,
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
897 xlabel="HD", nr_above_bars=nr_above_bars)
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
898
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
899 # 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
900 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
901 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
902 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
903
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
904 # 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
905 plotHDwithinSeq_Sum2(HDhalf1, HDhalf1min, HDhalf2, HDhalf2min, minHDs, pdf=pdf, lenTags=lenTags,
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
906 title_file1=name1)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
907
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
908 # 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
909 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
910 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
911 title_file1=name1, lenTags=lenTags,
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
912 xlabel="absolute delta HD", relative=False, nr_above_bars=nr_above_bars)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
913
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
914 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
915 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
916 title_file1=name1, lenTags=lenTags,
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
917 xlabel="relative delta HD", relative=True, nr_above_bars=nr_above_bars)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
918
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
919 # 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
920 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
921 # HD
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
922 plotHDwithFSD(listDifference1_zeros, maximumXDifference_zeros, minimumXDifference_zeros, pdf=pdf,
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
923 subtitle="Hamming distance of the non-identical half of chimeras",
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
924 title_file1=name1, lenTags=lenTags, xlabel="HD", relative=False,
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
925 nr_above_bars=nr_above_bars)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
926
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
927 # 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
928 # HD
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
929 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
930 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
931
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
932 # FSD
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
933 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
934 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
935
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
936 # 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
937 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
938 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
939
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
940 # HD
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
941 # absolute difference
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
942 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
943 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
944 # 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
945 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
946 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
947
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
948 # chimeric reads
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
949 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
950 # 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
951 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
952 overallSum15 = sum(sumCol15)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
953
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
954 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
955 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
956 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
957
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
958 # HD
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
959 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
960 "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
961 # FSD
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
962 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
963 "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
964 diff=False)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
965
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
966 # 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
967 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
968 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
969 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
970 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
971 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
972 "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
973
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
974 # 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
975 output_file.write(
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
976 "The hamming distances were calculated by comparing each half of all tags against the tag(s) with the minimum Hamming distance per half.\n"
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
977 "It is possible that one tag can have the minimum HD from multiple tags, so the sample size in this calculation differs from the sample size entered by the user.\n")
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
978 output_file.write(
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
979 "actual number of tags with min HD = {:,} (sample size by user = {:,})\n".format(
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
980 len(numpy.concatenate(listDifference1)), len(numpy.concatenate(list1))))
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
981 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
982
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
983 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
984 "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
985 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
986 "Absolute delta Hamming distances within 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
987 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
988 "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
989
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
990 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
991 output_file.write(
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
992 "Chimeras:\nAll tags were filtered: only those tags where at least one half is identical with the half of the min. tag are kept.\nSo the hamming distance of the non-identical half is compared.\n")
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
993 createFileHD(summary15, sumCol15, overallSum15, output_file,
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
994 "Hamming distances of non-zero half", sep)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
995 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
996
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
997
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
998 if __name__ == '__main__':
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
999 sys.exit(Hamming_Distance_Analysis(sys.argv))