Mercurial > repos > mheinzl > fsd
annotate fsd.py @ 28:94df985e2a93 draft
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
author | mheinzl |
---|---|
date | Mon, 03 Jun 2019 06:07:30 -0400 |
parents | b2b1f44966cb |
children | f77566cfa5e1 |
rev | line source |
---|---|
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
1 #!/usr/bin/env python |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
2 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
3 # Family size distribution of SSCSs |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
4 # |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
5 # Author: Monika Heinzl, Johannes-Kepler University Linz (Austria) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
6 # Contact: monika.heinzl@edumail.at |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
7 # |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
8 # Takes at least one TABULAR file with tags before the alignment to the SSCS, but up to 4 files can be provided, as input. |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
9 # The program produces a plot which shows the distribution of family sizes of the all SSCSs from the input files and |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
10 # a tabular file with the data of the plot, as well as a TXT file with all tags of the DCS and their family sizes. |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
11 # If only one file is provided, then a family size distribution, which is separated after SSCSs without a partner and DCSs, is produced. |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
12 # Whereas a family size distribution with multiple data in one plot is produced, when more than one file (up to 4) is given. |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
13 |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
14 # USAGE: python FSD_Galaxy_1.4_commandLine_FINAL.py --inputFile1 filename --inputName1 filename --inputFile2 filename2 --inputName2 filename2 --inputFile3 filename3 --inputName3 filename3 --inputFile4 filename4 --inputName4 filename4 --log_axis --output_tabular outptufile_name_tabular --output_pdf outptufile_name_pdf |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
15 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
16 import argparse |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
17 import sys |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
18 import os |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
19 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
20 import matplotlib.pyplot as plt |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
21 import numpy |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
22 from matplotlib.backends.backend_pdf import PdfPages |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
23 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
24 plt.switch_backend('agg') |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
25 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
26 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
27 def readFileReferenceFree(file): |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
28 with open(file, 'r') as dest_f: |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
29 data_array = numpy.genfromtxt(dest_f, skip_header=0, delimiter='\t', comments='#', dtype='string') |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
30 return(data_array) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
31 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
32 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
33 def make_argparser(): |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
34 parser = argparse.ArgumentParser(description='Family Size Distribution of duplex sequencing data') |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
35 parser.add_argument('--inputFile1', help='Tabular File with three columns: ab or ba, tag and family size.') |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
36 parser.add_argument('--inputName1') |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
37 parser.add_argument('--inputFile2', default=None, help='Tabular File with three columns: ab or ba, tag and family size.') |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
38 parser.add_argument('--inputName2') |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
39 parser.add_argument('--inputFile3', default=None, help='Tabular File with three columns: ab or ba, tag and family size.') |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
40 parser.add_argument('--inputName3') |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
41 parser.add_argument('--inputFile4', default=None, help='Tabular File with three columns: ab or ba, tag and family size.') |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
42 parser.add_argument('--inputName4') |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
43 parser.add_argument('--log_axis', action="store_false", help='Transform y axis in log scale.') |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
44 parser.add_argument('--output_pdf', default="data.pdf", type=str, help='Name of the pdf file.') |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
45 parser.add_argument('--output_tabular', default="data.tabular", type=str, help='Name of the tabular file.') |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
46 return parser |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
47 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
48 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
49 def compare_read_families(argv): |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
50 |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
51 parser = make_argparser() |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
52 args = parser.parse_args(argv[1:]) |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
53 |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
54 firstFile = args.inputFile1 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
55 name1 = args.inputName1 |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
56 |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
57 secondFile = args.inputFile2 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
58 name2 = args.inputName2 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
59 thirdFile = args.inputFile3 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
60 name3 = args.inputName3 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
61 fourthFile = args.inputFile4 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
62 name4 = args.inputName4 |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
63 log_axis = args.log_axis |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
64 |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
65 title_file = args.output_tabular |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
66 title_file2 = args.output_pdf |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
67 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
68 sep = "\t" |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
69 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
70 plt.rc('figure', figsize=(11.69, 8.27)) # A4 format |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
71 plt.rcParams['patch.edgecolor'] = "black" |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
72 plt.rcParams['axes.facecolor'] = "E0E0E0" # grey background color |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
73 plt.rcParams['xtick.labelsize'] = 14 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
74 plt.rcParams['ytick.labelsize'] = 14 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
75 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
76 list_to_plot = [] |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
77 label = [] |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
78 data_array_list = [] |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
79 list_to_plot_original = [] |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
80 colors = [] |
21
89ddbe5ae2aa
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
20
diff
changeset
|
81 bins = numpy.arange(1, 22) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
82 with open(title_file, "w") as output_file, PdfPages(title_file2) as pdf: |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
83 fig = plt.figure() |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
84 fig.subplots_adjust(left=0.12, right=0.97, bottom=0.23, top=0.94, hspace=0) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
85 fig2 = plt.figure() |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
86 fig2.subplots_adjust(left=0.12, right=0.97, bottom=0.23, top=0.94, hspace=0) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
87 |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
88 # plt.subplots_adjust(bottom=0.25) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
89 if firstFile != str(None): |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
90 file1 = readFileReferenceFree(firstFile) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
91 integers = numpy.array(file1[:, 0]).astype(int) # keep original family sizes |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
92 list_to_plot_original.append(integers) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
93 colors.append("#0000FF") |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
94 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
95 # for plot: replace all big family sizes by 22 |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
96 # data1 = numpy.array(file1[:, 0]).astype(int) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
97 # bigFamilies = numpy.where(data1 > 20)[0] |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
98 # data1[bigFamilies] = 22 |
20
64f0362c974e
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
19
diff
changeset
|
99 data1 = numpy.clip(integers, bins[0], bins[-1]) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
100 name1 = name1.split(".tabular")[0] |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
101 list_to_plot.append(data1) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
102 label.append(name1) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
103 data_array_list.append(file1) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
104 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
105 legend = "\n\n\n{}".format(name1) |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
106 fig.text(0.05, 0.11, legend, size=10, transform=plt.gcf().transFigure) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
107 fig2.text(0.05, 0.11, legend, size=10, transform=plt.gcf().transFigure) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
108 |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
109 legend1 = "singletons:\nnr. of tags\n{:,} ({:.3f})".format(numpy.bincount(data1)[1], float(numpy.bincount(data1)[1]) / len(data1)) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
110 fig.text(0.32, 0.11, legend1, size=10, transform=plt.gcf().transFigure) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
111 fig2.text(0.32, 0.11, legend1, size=10, transform=plt.gcf().transFigure) |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
112 |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
113 legend3b = "PE reads\n{:,} ({:.3f})".format(numpy.bincount(data1)[1], float(numpy.bincount(data1)[1]) / sum(integers)) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
114 fig.text(0.45, 0.11, legend3b, size=10, transform=plt.gcf().transFigure) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
115 fig2.text(0.45, 0.11, legend3b, size=10, transform=plt.gcf().transFigure) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
116 |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
117 legend4 = "family size > 20:\nnr. of tags\n{:,} ({:.3f})".format(numpy.bincount(data1)[len(numpy.bincount(data1)) - 1].astype(int), float(numpy.bincount(data1)[len(numpy.bincount(data1)) - 1]) / len(data1)) |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
118 fig.text(0.58, 0.11, legend4, size=10, transform=plt.gcf().transFigure) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
119 fig2.text(0.58, 0.11, legend4, size=10, transform=plt.gcf().transFigure) |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
120 |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
121 legend5 = "PE reads\n{:,} ({:.3f})".format(sum(integers[integers > 20]), float(sum(integers[integers > 20])) / sum(integers)) |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
122 fig.text(0.70, 0.11, legend5, size=10, transform=plt.gcf().transFigure) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
123 fig2.text(0.70, 0.11, legend5, size=10, transform=plt.gcf().transFigure) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
124 |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
125 legend6 = "total nr. of\ntags\n{:,}".format(len(data1)) |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
126 fig.text(0.82, 0.11, legend6, size=10, transform=plt.gcf().transFigure) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
127 fig2.text(0.82, 0.11, legend6, size=10, transform=plt.gcf().transFigure) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
128 |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
129 legend6b = "PE reads\n{:,}".format(sum(integers)) |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
130 fig.text(0.89, 0.11, legend6b, size=10, transform=plt.gcf().transFigure) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
131 fig2.text(0.89, 0.11, legend6b, size=10, transform=plt.gcf().transFigure) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
132 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
133 if secondFile != str(None): |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
134 file2 = readFileReferenceFree(secondFile) |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
135 integers2 = numpy.array(file2[:, 0]).astype(int) # keep original family sizes |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
136 list_to_plot_original.append(integers2) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
137 colors.append("#298A08") |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
138 |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
139 # data2 = numpy.asarray(file2[:, 0]).astype(int) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
140 # bigFamilies2 = numpy.where(data2 > 20)[0] |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
141 # data2[bigFamilies2] = 22 |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
142 |
20
64f0362c974e
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
19
diff
changeset
|
143 data2 = numpy.clip(integers2, bins[0], bins[-1]) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
144 list_to_plot.append(data2) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
145 name2 = name2.split(".tabular")[0] |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
146 label.append(name2) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
147 data_array_list.append(file2) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
148 |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
149 fig.text(0.05, 0.09, name2, size=10, transform=plt.gcf().transFigure) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
150 fig2.text(0.05, 0.09, name2, size=10, transform=plt.gcf().transFigure) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
151 |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
152 legend1 = "{:,} ({:.3f})".format(numpy.bincount(data2)[1], float(numpy.bincount(data2)[1]) / len(data2)) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
153 fig.text(0.32, 0.09, legend1, size=10, transform=plt.gcf().transFigure) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
154 fig2.text(0.32, 0.09, legend1, size=10, transform=plt.gcf().transFigure) |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
155 |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
156 legend3 = "{:,} ({:.3f})".format(numpy.bincount(data2)[1], float(numpy.bincount(data2)[1]) / sum(integers2)) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
157 fig.text(0.45, 0.09, legend3, size=10, transform=plt.gcf().transFigure) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
158 fig2.text(0.45, 0.09, legend3, size=10, transform=plt.gcf().transFigure) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
159 |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
160 legend4 = "{:,} ({:.3f})".format( |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
161 numpy.bincount(data2)[len(numpy.bincount(data2)) - 1].astype(int), |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
162 float(numpy.bincount(data2)[len(numpy.bincount(data2)) - 1]) / len(data2)) |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
163 fig.text(0.58, 0.09, legend4, size=10, transform=plt.gcf().transFigure) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
164 fig2.text(0.58, 0.09, legend4, size=10, transform=plt.gcf().transFigure) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
165 |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
166 legend5 = "{:,} ({:.3f})".format(sum(integers2[integers2 > 20]), float(sum(integers2[integers2 > 20])) / sum(integers2)) |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
167 fig.text(0.70, 0.09, legend5, size=10, transform=plt.gcf().transFigure) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
168 fig2.text(0.70, 0.09, legend5, size=10, transform=plt.gcf().transFigure) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
169 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
170 legend6 = "{:,}".format(len(data2)) |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
171 fig.text(0.82, 0.09, legend6, size=10, transform=plt.gcf().transFigure) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
172 fig2.text(0.82, 0.09, legend6, size=10, transform=plt.gcf().transFigure) |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
173 |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
174 legend6b = "{:,}".format(sum(integers2)) |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
175 fig.text(0.89, 0.09, legend6b, size=10, transform=plt.gcf().transFigure) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
176 fig2.text(0.89, 0.09, legend6b, size=10, transform=plt.gcf().transFigure) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
177 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
178 if thirdFile != str(None): |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
179 file3 = readFileReferenceFree(thirdFile) |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
180 integers3 = numpy.array(file3[:, 0]).astype(int) # keep original family sizes |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
181 list_to_plot_original.append(integers3) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
182 colors.append("#DF0101") |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
183 |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
184 # data3 = numpy.asarray(file3[:, 0]).astype(int) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
185 # bigFamilies3 = numpy.where(data3 > 20)[0] |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
186 # data3[bigFamilies3] = 22 |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
187 |
20
64f0362c974e
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
19
diff
changeset
|
188 data3 = numpy.clip(integers3, bins[0], bins[-1]) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
189 list_to_plot.append(data3) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
190 name3 = name3.split(".tabular")[0] |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
191 label.append(name3) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
192 data_array_list.append(file3) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
193 |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
194 fig.text(0.05, 0.07, name3, size=10, transform=plt.gcf().transFigure) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
195 fig2.text(0.05, 0.07, name3, size=10, transform=plt.gcf().transFigure) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
196 |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
197 legend1 = "{:,} ({:.3f})".format(numpy.bincount(data3)[1], float(numpy.bincount(data3)[1]) / len(data3)) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
198 fig.text(0.32, 0.07, legend1, size=10, transform=plt.gcf().transFigure) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
199 fig2.text(0.32, 0.07, legend1, size=10, transform=plt.gcf().transFigure) |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
200 |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
201 legend3b = "{:,} ({:.3f})".format(numpy.bincount(data3)[1], float(numpy.bincount(data3)[1]) / sum(integers3)) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
202 fig.text(0.45, 0.07, legend3b, size=10, transform=plt.gcf().transFigure) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
203 fig2.text(0.45, 0.07, legend3b, size=10, transform=plt.gcf().transFigure) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
204 |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
205 legend4 = "{:,} ({:.3f})".format( |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
206 numpy.bincount(data3)[len(numpy.bincount(data3)) - 1].astype(int), |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
207 float(numpy.bincount(data3)[len(numpy.bincount(data3)) - 1]) / len(data3)) |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
208 fig.text(0.58, 0.07, legend4, size=10, transform=plt.gcf().transFigure) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
209 fig2.text(0.58, 0.07, legend4, size=10, transform=plt.gcf().transFigure) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
210 |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
211 legend5 = "{:,} ({:.3f})".format(sum(integers3[integers3 > 20]), |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
212 float(sum(integers3[integers3 > 20])) / sum(integers3)) |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
213 fig.text(0.70, 0.07, legend5, size=10, transform=plt.gcf().transFigure) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
214 fig2.text(0.70, 0.07, legend5, size=10, transform=plt.gcf().transFigure) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
215 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
216 legend6 = "{:,}".format(len(data3)) |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
217 fig.text(0.82, 0.07, legend6, size=10, transform=plt.gcf().transFigure) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
218 fig2.text(0.82, 0.07, legend6, size=10, transform=plt.gcf().transFigure) |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
219 |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
220 legend6b = "{:,}".format(sum(integers3)) |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
221 fig.text(0.89, 0.07, legend6b, size=10, transform=plt.gcf().transFigure) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
222 fig2.text(0.89, 0.07, legend6b, size=10, transform=plt.gcf().transFigure) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
223 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
224 if fourthFile != str(None): |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
225 file4 = readFileReferenceFree(fourthFile) |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
226 integers4 = numpy.array(file4[:, 0]).astype(int) # keep original family sizes |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
227 list_to_plot_original.append(integers4) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
228 colors.append("#04cec7") |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
229 |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
230 # data4 = numpy.asarray(file4[:, 0]).astype(int) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
231 # bigFamilies4 = numpy.where(data4 > 20)[0] |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
232 # data4[bigFamilies4] = 22 |
20
64f0362c974e
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
19
diff
changeset
|
233 data4 = numpy.clip(integers4, bins[0], bins[-1]) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
234 list_to_plot.append(data4) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
235 name4 = name4.split(".tabular")[0] |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
236 label.append(name4) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
237 data_array_list.append(file4) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
238 |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
239 fig.text(0.05, 0.05, name4, size=10, transform=plt.gcf().transFigure) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
240 fig2.text(0.05, 0.05, name4, size=10, transform=plt.gcf().transFigure) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
241 |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
242 legend1 = "{:,} ({:.3f})".format(numpy.bincount(data4)[1], float(numpy.bincount(data4)[1]) / len(data4)) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
243 fig.text(0.32, 0.05, legend1, size=10, transform=plt.gcf().transFigure) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
244 fig2.text(0.32, 0.05, legend1, size=10, transform=plt.gcf().transFigure) |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
245 |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
246 legend3b = "{:,} ({:.3f})".format(numpy.bincount(data4)[1], float(numpy.bincount(data4)[1]) / sum(integers4)) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
247 fig.text(0.45, 0.05, legend3b, size=10, transform=plt.gcf().transFigure) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
248 fig2.text(0.45, 0.05, legend3b, size=10, transform=plt.gcf().transFigure) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
249 |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
250 legend4 = "{:,} ({:.3f})".format( |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
251 numpy.bincount(data4)[len(numpy.bincount(data4)) - 1].astype(int), |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
252 float(numpy.bincount(data4)[len(numpy.bincount(data4)) - 1]) / len(data4)) |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
253 fig.text(0.58, 0.05, legend4, size=10, transform=plt.gcf().transFigure) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
254 fig2.text(0.58, 0.05, legend4, size=10, transform=plt.gcf().transFigure) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
255 |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
256 legend5 = "{:,} ({:.3f})".format(sum(integers4[integers4 > 20]), |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
257 float(sum(integers4[integers4 > 20])) / sum(integers4)) |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
258 fig.text(0.70, 0.05, legend5, size=10, transform=plt.gcf().transFigure) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
259 fig2.text(0.70, 0.05, legend5, size=10, transform=plt.gcf().transFigure) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
260 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
261 legend6 = "{:,}".format(len(data4)) |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
262 fig.text(0.82, 0.05, legend6, size=10, transform=plt.gcf().transFigure) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
263 fig2.text(0.82, 0.05, legend6, size=10, transform=plt.gcf().transFigure) |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
264 |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
265 legend6b = "{:,}".format(sum(integers4)) |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
266 fig.text(0.89, 0.05, legend6b, size=10, transform=plt.gcf().transFigure) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
267 fig2.text(0.89, 0.05, legend6b, size=10, transform=plt.gcf().transFigure) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
268 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
269 maximumX = numpy.amax(numpy.concatenate(list_to_plot)) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
270 minimumX = numpy.amin(numpy.concatenate(list_to_plot)) |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
271 list_to_plot2 = list_to_plot |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
272 to_plot = ["Absolute frequencies", "Relative frequencies"] |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
273 plt.xticks([], []) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
274 plt.yticks([], []) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
275 fig.suptitle('Family Size Distribution (tags)', fontsize=14) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
276 |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
277 for l in range(len(to_plot)): |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
278 ax = fig.add_subplot(2, 1, l+1) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
279 ticks = numpy.arange(1, 22, 1) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
280 ticks1 = map(str, ticks) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
281 if maximumX > 20: |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
282 ticks1[len(ticks1) - 1] = ">20" |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
283 |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
284 if to_plot[l] == "Relative frequencies": |
21
89ddbe5ae2aa
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
20
diff
changeset
|
285 counts_rel = ax.hist(list_to_plot2, bins=numpy.arange(minimumX, maximumX + 2), stacked=False, edgecolor="black", linewidth=1, label=label, align="left", alpha=0.8, rwidth=0.8, normed=True) |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
286 else: |
21
89ddbe5ae2aa
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
20
diff
changeset
|
287 counts = ax.hist(list_to_plot2, bins=numpy.arange(minimumX, maximumX + 2), stacked=False, edgecolor="black", linewidth=1, label=label, align="left", alpha=0.8, rwidth=0.8) |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
288 ax.legend(loc='upper right', fontsize=14, frameon=True, bbox_to_anchor=(0.9, 1)) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
289 |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
290 ax.set_xticks(numpy.array(ticks)) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
291 ax.set_xticklabels(ticks1) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
292 |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
293 ax.set_ylabel(to_plot[l], fontsize=14) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
294 ax.set_xlabel("Family size", fontsize=14) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
295 if log_axis: |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
296 ax.set_yscale('log') |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
297 ax.grid(b=True, which="major", color="#424242", linestyle=":") |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
298 ax.margins(0.01, None) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
299 pdf.savefig(fig) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
300 plt.close() |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
301 |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
302 fig2.suptitle('Family Size Distribution (PE reads)', fontsize=14) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
303 for l in range(len(to_plot)): |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
304 ax = fig2.add_subplot(2, 1, l + 1) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
305 ticks = numpy.arange(minimumX, maximumX + 1) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
306 ticks1 = map(str, ticks) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
307 if maximumX > 20: |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
308 ticks1[len(ticks1) - 1] = ">20" |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
309 reads = [] |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
310 reads_rel = [] |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
311 |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
312 barWidth = 0 - (len(list_to_plot)+1)/2 * 1./(len(list_to_plot) + 1) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
313 |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
314 for i in range(len(list_to_plot2)): |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
315 unique, c = numpy.unique(list_to_plot2[i], return_counts=True) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
316 new_c = [] |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
317 new_unique = [] |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
318 for t in ticks: |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
319 if t not in unique: |
21
89ddbe5ae2aa
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
20
diff
changeset
|
320 new_c.append(0) # add zero count of not occuring |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
321 new_unique.append(t) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
322 else: |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
323 c_idx = numpy.where(t == unique)[0] |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
324 new_c.append(c[c_idx]) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
325 new_unique.append(unique[c_idx]) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
326 y = numpy.array(new_unique) * numpy.array(new_c) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
327 if len([list_to_plot_original > 20]) > 0: |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
328 y[len(y) - 1] = sum(list_to_plot_original[i][list_to_plot_original[i] > 20]) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
329 reads.append(y) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
330 reads_rel.append(list(numpy.float_(y)) / sum(y)) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
331 |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
332 x = list(numpy.arange(numpy.amin(unique), numpy.amax(unique) + 1).astype(float)) |
22
5e650e66e058
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
21
diff
changeset
|
333 if len(list_to_plot2) == 1: |
5e650e66e058
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
21
diff
changeset
|
334 x = [xi * 0.5 for xi in x] |
5e650e66e058
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
21
diff
changeset
|
335 w = 0.4 |
5e650e66e058
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
21
diff
changeset
|
336 else: |
5e650e66e058
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
21
diff
changeset
|
337 x = [xi + barWidth for xi in x] |
5e650e66e058
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
21
diff
changeset
|
338 w = 1./(len(list_to_plot) + 1) |
23
5ae4fd1d4a12
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
22
diff
changeset
|
339 |
24
807d893d04a7
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
23
diff
changeset
|
340 |
26
60f66f701816
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
25
diff
changeset
|
341 #print(label[i]) |
60f66f701816
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
25
diff
changeset
|
342 #print(colors[i]) |
60f66f701816
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
25
diff
changeset
|
343 #print(w) |
24
807d893d04a7
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
23
diff
changeset
|
344 # linewidth=1, |
26
60f66f701816
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
25
diff
changeset
|
345 |
27
b2b1f44966cb
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
26
diff
changeset
|
346 print(numpy.sum(y)) |
28
94df985e2a93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
27
diff
changeset
|
347 new_y = numpy.concatenate(numpy.array([yi / float(numpy.sum(y)) for yi in y])) |
94df985e2a93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
27
diff
changeset
|
348 #print(new_y) |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
349 |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
350 if to_plot[l] == "Relative frequencies": |
26
60f66f701816
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
25
diff
changeset
|
351 counts2_rel = ax.bar(x, new_y, align="edge", width=w, |
24
807d893d04a7
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
23
diff
changeset
|
352 edgecolor="black", label=label[i], alpha=0.8, color=colors[i]) |
23
5ae4fd1d4a12
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
22
diff
changeset
|
353 |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
354 else: |
22
5e650e66e058
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
21
diff
changeset
|
355 counts2 = ax.bar(x, y, align="edge", width=w, edgecolor="black", label=label[i], |
24
807d893d04a7
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
23
diff
changeset
|
356 alpha=0.8, color=colors[i]) |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
357 if i == len(list_to_plot2): |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
358 barWidth += 1. / (len(list_to_plot) + 1) + 1. / (len(list_to_plot) + 1) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
359 else: |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
360 barWidth += 1. / (len(list_to_plot) + 1) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
361 |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
362 if to_plot[l] == "Absolute frequencies": |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
363 ax.legend(loc='upper right', fontsize=14, frameon=True, bbox_to_anchor=(0.9, 1)) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
364 else: |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
365 ax.set_xlabel("Family size", fontsize=14) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
366 |
22
5e650e66e058
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
21
diff
changeset
|
367 if len(list_to_plot2) == 1: |
5e650e66e058
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
21
diff
changeset
|
368 ax.set_xticks(numpy.array([xi + 0.2 for xi in x])) |
5e650e66e058
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
21
diff
changeset
|
369 else: |
5e650e66e058
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
21
diff
changeset
|
370 ax.set_xticks(numpy.array(ticks)) |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
371 ax.set_xticklabels(ticks1) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
372 ax.set_ylabel(to_plot[l], fontsize=14) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
373 if log_axis: |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
374 ax.set_yscale('log') |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
375 ax.grid(b=True, which="major", color="#424242", linestyle=":") |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
376 ax.margins(0.01, None) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
377 |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
378 pdf.savefig(fig2) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
379 plt.close() |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
380 |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
381 # write data to CSV file tags |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
382 output_file.write("Values from family size distribution with all datasets (tags)\n") |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
383 output_file.write("\nFamily size") |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
384 for i in label: |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
385 output_file.write("{}{}".format(sep, i)) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
386 # output_file.write("{}sum".format(sep)) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
387 output_file.write("\n") |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
388 j = 0 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
389 for fs in counts[1][0:len(counts[1]) - 1]: |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
390 if fs == 21: |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
391 fs = ">20" |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
392 else: |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
393 fs = "={}".format(fs) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
394 output_file.write("FS{}{}".format(fs, sep)) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
395 if len(label) == 1: |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
396 output_file.write("{}{}".format(int(counts[0][j]), sep)) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
397 else: |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
398 for n in range(len(label)): |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
399 output_file.write("{}{}".format(int(counts[0][n][j]), sep)) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
400 output_file.write("\n") |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
401 j += 1 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
402 output_file.write("sum{}".format(sep)) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
403 if len(label) == 1: |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
404 output_file.write("{}{}".format(int(sum(counts[0])), sep)) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
405 else: |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
406 for i in counts[0]: |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
407 output_file.write("{}{}".format(int(sum(i)), sep)) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
408 |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
409 # write data to CSV file PE reads |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
410 output_file.write("\n\nValues from family size distribution with all datasets (PE reads)\n") |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
411 output_file.write("\nFamily size") |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
412 for i in label: |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
413 output_file.write("{}{}".format(sep, i)) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
414 # output_file.write("{}sum".format(sep)) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
415 output_file.write("\n") |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
416 j = 0 |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
417 for fs in bins: |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
418 if fs == 21: |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
419 fs = ">20" |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
420 else: |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
421 fs = "={}".format(fs) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
422 output_file.write("FS{}{}".format(fs, sep)) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
423 if len(label) == 1: |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
424 output_file.write("{}{}".format(int(reads[0][j]), sep)) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
425 else: |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
426 for n in range(len(label)): |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
427 output_file.write("{}{}".format(int(reads[n][j]), sep)) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
428 output_file.write("\n") |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
429 j += 1 |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
430 output_file.write("sum{}".format(sep)) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
431 if len(label) == 1: |
22
5e650e66e058
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
21
diff
changeset
|
432 output_file.write("{}{}".format(int(sum(numpy.concatenate(reads))), sep)) |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
433 else: |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
434 for i in reads: |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
435 output_file.write("{}{}".format(int(sum(i)), sep)) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
436 output_file.write("\n") |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
437 |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
438 # Family size distribution after DCS and SSCS |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
439 for dataset, data_o, name_file in zip(list_to_plot, data_array_list, label): |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
440 maximumX = numpy.amax(dataset) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
441 minimumX = numpy.amin(dataset) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
442 |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
443 tags = numpy.array(data_o[:, 2]) |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
444 seq = numpy.array(data_o[:, 1]) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
445 data = numpy.array(dataset) |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
446 data_o = numpy.array(data_o[:, 0]).astype(int) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
447 # find all unique tags and get the indices for ALL tags, but only once |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
448 u, index_unique, c = numpy.unique(numpy.array(seq), return_counts=True, return_index=True) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
449 d = u[c > 1] |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
450 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
451 # get family sizes, tag for duplicates |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
452 duplTags_double = data[numpy.in1d(seq, d)] |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
453 duplTags_double_o = data_o[numpy.in1d(seq, d)] |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
454 |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
455 duplTags = duplTags_double[0::2] # ab of DCS |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
456 duplTags_o = duplTags_double_o[0::2] # ab of DCS |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
457 |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
458 duplTagsBA = duplTags_double[1::2] # ba of DCS |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
459 duplTagsBA_o = duplTags_double_o[1::2] # ba of DCS |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
460 |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
461 # duplTags_double_tag = tags[numpy.in1d(seq, d)] |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
462 # duplTags_double_seq = seq[numpy.in1d(seq, d)] |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
463 |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
464 # get family sizes for SSCS with no partner |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
465 ab = numpy.where(tags == "ab")[0] |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
466 abSeq = seq[ab] |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
467 ab_o = data_o[ab] |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
468 ab = data[ab] |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
469 |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
470 ba = numpy.where(tags == "ba")[0] |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
471 baSeq = seq[ba] |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
472 ba_o = data_o[ba] |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
473 ba = data[ba] |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
474 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
475 dataAB = ab[numpy.in1d(abSeq, d, invert=True)] |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
476 dataAB_o = ab_o[numpy.in1d(abSeq, d, invert=True)] |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
477 |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
478 dataBA = ba[numpy.in1d(baSeq, d, invert=True)] |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
479 dataBA_o = ba_o[numpy.in1d(baSeq, d, invert=True)] |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
480 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
481 list1 = [duplTags_double, dataAB, dataBA] # list for plotting |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
482 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
483 # information for family size >= 3 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
484 dataAB_FS3 = dataAB[dataAB >= 3] |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
485 dataAB_FS3_o = dataAB_o[dataAB_o >= 3] |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
486 dataBA_FS3 = dataBA[dataBA >= 3] |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
487 dataBA_FS3_o = dataBA_o[dataBA_o >= 3] |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
488 # ab_FS3 = ab[ab >= 3] |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
489 # ba_FS3 = ba[ba >= 3] |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
490 # ab_FS3_o = ab_o[ab_o >= 3] |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
491 # ba_FS3_o = ba_o[ba_o >= 3] |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
492 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
493 duplTags_FS3 = duplTags[(duplTags >= 3) & (duplTagsBA >= 3)] # ab+ba with FS>=3 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
494 duplTags_FS3_BA = duplTagsBA[(duplTags >= 3) & (duplTagsBA >= 3)] # ba+ab with FS>=3 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
495 duplTags_double_FS3 = len(duplTags_FS3) + len(duplTags_FS3_BA) # both ab and ba strands with FS>=3 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
496 |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
497 # original FS |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
498 duplTags_FS3_o = duplTags_o[(duplTags_o >= 3) & (duplTagsBA_o >= 3)] # ab+ba with FS>=3 |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
499 duplTags_FS3_BA_o = duplTagsBA_o[(duplTags_o >= 3) & (duplTagsBA_o >= 3)] # ba+ab with FS>=3 |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
500 duplTags_double_FS3_o = sum(duplTags_FS3_o) + sum(duplTags_FS3_BA_o) # both ab and ba strands with FS>=3 |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
501 |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
502 fig = plt.figure() |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
503 plt.subplots_adjust(left=0.12, right=0.97, bottom=0.3, top=0.94, hspace=0) |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
504 counts = plt.hist(list1, bins=numpy.arange(minimumX, maximumX + 2), stacked=True, label=["duplex", "ab", "ba"], |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
505 edgecolor="black", linewidth=1, align="left", color=["#FF0000", "#5FB404", "#FFBF00"], |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
506 rwidth=0.8) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
507 # tick labels of x axis |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
508 ticks = numpy.arange(1, 22, 1) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
509 ticks1 = map(str, ticks) |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
510 if maximumX > 20: |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
511 ticks1[len(ticks1) - 1] = ">20" |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
512 plt.xticks(numpy.array(ticks), ticks1) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
513 singl = counts[0][2][0] # singletons |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
514 last = counts[0][2][len(counts[0][0]) - 1] # large families |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
515 if log_axis: |
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
516 plt.yscale('log') |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
517 plt.legend(loc='upper right', fontsize=14, bbox_to_anchor=(0.9, 1), frameon=True) |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
518 plt.title(name_file, fontsize=14) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
519 plt.xlabel("Family size", fontsize=14) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
520 plt.ylabel("Absolute Frequency", fontsize=14) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
521 plt.margins(0.01, None) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
522 plt.grid(b=True, which="major", color="#424242", linestyle=":") |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
523 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
524 # extra information beneath the plot |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
525 legend = "SSCS ab= \nSSCS ba= \nDCS (total)= \ntotal nr. of tags=" |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
526 plt.text(0.1, 0.09, legend, size=10, transform=plt.gcf().transFigure) |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
527 |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
528 legend = "nr. of tags\n\n{:,}\n{:,}\n{:,} ({:,})\n{:,}".format(len(dataAB), len(dataBA), len(duplTags), len(duplTags_double), (len(dataAB) + len(dataBA) + len(duplTags))) |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
529 plt.text(0.23, 0.09, legend, size=10, transform=plt.gcf().transFigure) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
530 |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
531 legend5 = "PE reads\n\n{:,}\n{:,}\n{:,} ({:,})\n{:,}".format(sum(dataAB_o), sum(dataBA_o), sum(duplTags_o), sum(duplTags_double_o), (sum(dataAB_o) + sum(dataBA_o) + sum(duplTags_o))) |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
532 plt.text(0.38, 0.09, legend5, size=10, transform=plt.gcf().transFigure) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
533 |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
534 legend = "rel. freq. of tags\nunique\n{:.3f}\n{:.3f}\n{:.3f}\n{:,}".format(float(len(dataAB)) / (len(dataAB) + len(dataBA) + len(duplTags)), float(len(dataBA)) / (len(dataAB) + len(dataBA) + len(duplTags)), float(len(duplTags)) / (len(dataAB) + len(dataBA) + len(duplTags)), (len(dataAB) + len(dataBA) + len(duplTags))) |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
535 plt.text(0.54, 0.09, legend, size=10, transform=plt.gcf().transFigure) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
536 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
537 legend = "total\n{:.3f}\n{:.3f}\n{:.3f} ({:.3f})\n{:,}".format(float(len(dataAB)) / (len(ab) + len(ba)), float(len(dataBA)) / (len(ab) + len(ba)), float(len(duplTags)) / (len(ab) + len(ba)), float(len(duplTags_double)) / (len(ab) + len(ba)), (len(ab) + len(ba))) |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
538 plt.text(0.64, 0.09, legend, size=10, transform=plt.gcf().transFigure) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
539 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
540 legend1 = "\nsingletons:\nfamily size > 20:" |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
541 plt.text(0.1, 0.03, legend1, size=10, transform=plt.gcf().transFigure) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
542 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
543 legend4 = "{:,}\n{:,}".format(singl.astype(int), last.astype(int)) |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
544 plt.text(0.23, 0.03, legend4, size=10, transform=plt.gcf().transFigure) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
545 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
546 legend3 = "{:.3f}\n{:.3f}".format(singl / len(data), last / len(data)) |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
547 plt.text(0.64, 0.03, legend3, size=10, transform=plt.gcf().transFigure) |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
548 |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
549 legend3 = "\n\n{:,}".format(sum(data_o[data_o > 20])) |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
550 plt.text(0.38, 0.03, legend3, size=10, transform=plt.gcf().transFigure) |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
551 |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
552 legend3 = "{:.3f}\n{:.3f}".format(float(singl)/sum(data_o), float(sum(data_o[data_o > 20])) / sum(data_o)) |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
553 plt.text(0.84, 0.03, legend3, size=10, transform=plt.gcf().transFigure) |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
554 |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
555 legend = "PE reads\nunique\n{:.3f}\n{:.3f}\n{:.3f}\n{:,}".format( |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
556 float(sum(dataAB_o)) / (sum(dataAB_o) + sum(dataBA_o) + sum(duplTags_o)), |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
557 float(sum(dataBA_o)) / (sum(dataAB_o) + sum(dataBA_o) + sum(duplTags_o)), |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
558 float(sum(duplTags_o)) / (sum(dataAB_o) + sum(dataBA_o) + sum(duplTags_o)), |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
559 (sum(dataAB_o) + sum(dataBA_o) + sum(duplTags_o))) |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
560 plt.text(0.74, 0.09, legend, size=10, transform=plt.gcf().transFigure) |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
561 |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
562 legend = "total\n{:.3f}\n{:.3f}\n{:.3f} ({:.3f})\n{:,}".format( |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
563 float(sum(dataAB_o)) / (sum(ab_o) + sum(ba_o)), |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
564 float(sum(dataBA_o)) / (sum(ab_o) + sum(ba_o)), |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
565 float(sum(duplTags_o)) / (sum(ab_o) + sum(ba_o)), |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
566 float(sum(duplTags_double_o)) / (sum(ab_o) + sum(ba_o)), (sum(ab_o) + sum(ba_o))) |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
567 plt.text(0.84, 0.09, legend, size=10, transform=plt.gcf().transFigure) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
568 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
569 pdf.savefig(fig) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
570 plt.close() |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
571 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
572 # write same information to a csv file |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
573 count = numpy.bincount(integers) # original counts of family sizes |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
574 output_file.write("\nDataset:{}{}\n".format(sep, name_file)) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
575 output_file.write("max. family size:{}{}\n".format(sep, max(integers))) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
576 output_file.write("absolute frequency:{}{}\n".format(sep, count[len(count) - 1])) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
577 output_file.write("relative frequency:{}{:.3f}\n\n".format(sep, float(count[len(count) - 1]) / sum(count))) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
578 |
18
c825a29a7d9f
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
17
diff
changeset
|
579 output_file.write("{}singletons:{}{}{}family size > 20:{}{}{}{}length of dataset:\n".format(sep, sep, sep, sep, sep, sep, sep, sep)) |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
580 output_file.write("{}nr. of tags{}rel. freq of tags{}rel.freq of PE reads{}nr. of tags{}rel. freq of tags{}nr. of PE reads{}rel. freq of PE reads{}total nr. of tags{}total nr. of PE reads\n".format(sep, sep, sep, sep, sep, sep, sep, sep, sep)) |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
581 output_file.write("{}{}{}{}{:.3f}{}{:.3f}{}{}{}{:.3f}{}{}{}{:.3f}{}{}{}{}\n\n".format( |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
582 name_file, sep, singl.astype(int), sep, singl / len(data), sep, float(singl)/sum(data_o), sep, |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
583 last.astype(int), sep, last / len(data), sep, sum(data_o[data_o > 20]), sep, float(sum(data_o[data_o > 20])) / sum(data_o), sep, len(data), sep, sum(data_o))) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
584 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
585 # information for FS >= 1 |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
586 output_file.write("The unique frequencies were calculated from the dataset where the tags occured only once (=ab without DCS, ba without DCS)\n" |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
587 "Whereas the total frequencies were calculated from the whole dataset (=including the DCS).\n\n") |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
588 output_file.write("FS >= 1{}nr. of tags{}nr. of PE reads{}rel. freq of tags{}{}rel. freq of PE reads:\n".format(sep, sep, sep, sep, sep)) |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
589 output_file.write("{}{}{}unique:{}total{}unique{}total:\n".format(sep, sep, sep, sep, sep, sep)) |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
590 output_file.write("SSCS ab{}{}{}{}{}{:.3f}{}{:.3f}{}{:.3f}{}{:.3f}\n".format( |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
591 sep, len(dataAB), sep, sum(dataAB_o), sep, float(len(dataAB)) / (len(dataAB) + len(dataBA) + len(duplTags)), |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
592 sep, float(sum(dataAB_o)) / (sum(dataAB_o) + sum(dataBA_o) + sum(duplTags_o)), sep, |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
593 float(len(dataAB)) / (len(ab) + len(ba)), sep, float(sum(dataAB_o)) / (sum(ab_o) + sum(ba_o)))) |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
594 output_file.write("SSCS ba{}{}{}{}{}{:.3f}{}{:.3f}{}{:.3f}{}{:.3f}\n".format( |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
595 sep, len(dataBA), sep, sum(dataBA_o), sep, float(len(dataBA)) / (len(dataBA) + len(dataBA) + len(duplTags)), |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
596 sep, float(sum(dataBA_o)) / (sum(dataBA_o) + sum(dataBA_o) + sum(duplTags_o)), sep, float(len(dataBA)) / (len(ba) + len(ba)), |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
597 sep, float(sum(dataBA_o)) / (sum(ba_o) + sum(ba_o)))) |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
598 output_file.write("DCS (total){}{} ({}){}{} ({}){}{:.3f}{}{:.3f} ({:.3f}){}{:.3f}{}{:.3f} ({:.3f})\n".format( |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
599 sep, len(duplTags), len(duplTags_double), sep, sum(duplTags_o), sum(duplTags_double_o), sep, |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
600 float(len(duplTags)) / (len(dataAB) + len(dataBA) + len(duplTags)), sep, |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
601 float(len(duplTags)) / (len(ab) + len(ba)), float(len(duplTags_double)) / (len(ab) + len(ba)), sep, |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
602 float(sum(duplTags_o)) / (sum(dataAB_o) + sum(dataBA_o) + sum(duplTags_o)), sep, |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
603 float(sum(duplTags_o)) / (sum(ab_o) + sum(ba_o)), float(sum(duplTags_double_o)) / (sum(ab_o) + sum(ba_o)))) |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
604 output_file.write("total nr. of tags{}{}{}{}{}{}{}{}{}{}{}{}\n".format( |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
605 sep, (len(dataAB) + len(dataBA) + len(duplTags)), sep, (sum(dataAB_o) + sum(dataBA_o) + sum(duplTags_o)), sep, |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
606 (len(dataAB) + len(dataBA) + len(duplTags)), sep, (len(ab) + len(ba)), sep, |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
607 (sum(dataAB_o) + sum(dataBA_o) + sum(duplTags_o)), sep, (sum(ab_o) + sum(ba_o)))) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
608 # information for FS >= 3 |
17
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
609 output_file.write("\nFS >= 3{}nr. of tags{}nr. of PE reads{}rel. freq of tags{}{}rel. freq of PE reads:\n".format(sep, sep, sep, sep, sep)) |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
610 output_file.write("{}{}{}unique:{}total{}unique{}total:\n".format(sep, sep, sep, sep, sep, sep)) |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
611 output_file.write("SSCS ab{}{}{}{}{}{:.3f}{}{:.3f}{}{:.3f}{}{:.3f}\n".format( |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
612 sep, len(dataAB_FS3), sep, sum(dataAB_FS3_o), sep, |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
613 float(len(dataAB_FS3)) / (len(dataAB_FS3) + len(dataBA_FS3) + len(duplTags_FS3)), sep, |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
614 float(len(dataAB_FS3)) / (len(dataBA_FS3) + len(dataBA_FS3) + duplTags_double_FS3), |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
615 sep, float(sum(dataAB_FS3_o)) / (sum(dataAB_FS3_o) + sum(dataBA_FS3_o) + sum(duplTags_FS3_o)), |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
616 sep, float(sum(dataAB_FS3_o)) / (sum(dataBA_FS3_o) + sum(dataBA_FS3_o) + duplTags_double_FS3_o))) |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
617 output_file.write("SSCS ba{}{}{}{}{}{:.3f}{}{:.3f}{}{:.3f}{}{:.3f}\n".format( |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
618 sep, len(dataBA_FS3), sep, sum(dataBA_FS3_o), sep, |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
619 float(len(dataBA_FS3)) / (len(dataBA_FS3) + len(dataBA_FS3) + len(duplTags_FS3)), |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
620 sep, float(len(dataBA_FS3)) / (len(dataBA_FS3) + len(dataBA_FS3) + duplTags_double_FS3), |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
621 sep, float(sum(dataBA_FS3_o)) / (sum(dataBA_FS3_o) + sum(dataBA_FS3_o) + sum(duplTags_FS3_o)), |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
622 sep, float(sum(dataBA_FS3_o)) / (sum(dataBA_FS3_o) + sum(dataBA_FS3_o) + duplTags_double_FS3_o))) |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
623 output_file.write("DCS (total){}{} ({}){}{} ({}){}{:.3f}{}{:.3f} ({:.3f}){}{:.3f}{}{:.3f} ({:.3f})\n".format( |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
624 sep, len(duplTags_FS3), duplTags_double_FS3, sep, sum(duplTags_FS3_o), duplTags_double_FS3_o, sep, |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
625 float(len(duplTags_FS3)) / (len(dataAB_FS3) + len(dataBA_FS3) + len(duplTags_FS3)), sep, |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
626 float(len(duplTags_FS3)) / (len(dataAB_FS3) + len(dataBA_FS3) + duplTags_double_FS3), |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
627 float(duplTags_double_FS3) / (len(dataAB_FS3) + len(dataBA_FS3) + duplTags_double_FS3), |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
628 sep, float(sum(duplTags_FS3_o)) / (sum(dataAB_FS3_o) + sum(dataBA_FS3_o) + sum(duplTags_FS3_o)), sep, |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
629 float(sum(duplTags_FS3_o)) / (sum(dataAB_FS3_o) + sum(dataBA_FS3_o) + duplTags_double_FS3_o), |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
630 float(duplTags_double_FS3_o) / (sum(dataAB_FS3_o) + sum(dataBA_FS3_o) + duplTags_double_FS3_o))) |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
631 output_file.write("total nr. of tags{}{}{}{}{}{}{}{}{}{}{}{}\n".format( |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
632 sep, (len(dataAB_FS3) + len(dataBA_FS3) + len(duplTags_FS3)), sep, (sum(dataAB_FS3_o) + sum(dataBA_FS3_o) + sum(duplTags_FS3_o)), |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
633 sep, (len(dataAB_FS3) + len(dataBA_FS3) + len(duplTags_FS3)), sep, (len(dataAB_FS3) + len(dataBA_FS3) + duplTags_double_FS3), |
2e517a54eedc
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
16
diff
changeset
|
634 sep, (sum(dataAB_FS3_o) + sum(dataBA_FS3_o) + sum(duplTags_FS3_o)), sep, (sum(dataAB_FS3_o) + sum(dataBA_FS3_o) + duplTags_double_FS3_o))) |
16
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
635 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
636 output_file.write("\nValues from family size distribution\n") |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
637 output_file.write("{}duplex{}ab{}ba{}sum\n".format(sep, sep, sep, sep)) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
638 for dx, ab, ba, fs in zip(counts[0][0], counts[0][1], counts[0][2], counts[1]): |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
639 if fs == 21: |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
640 fs = ">20" |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
641 else: |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
642 fs = "={}".format(fs) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
643 ab1 = ab - dx |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
644 ba1 = ba - ab |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
645 output_file.write("FS{}{}{}{}{}{}{}{}{}\n".format(fs, sep, int(dx), sep, int(ab1), sep, int(ba1), sep, int(ba))) |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
646 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
647 print("Files successfully created!") |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
648 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
649 |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
650 if __name__ == '__main__': |
6bd9ef49d013
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a
mheinzl
parents:
diff
changeset
|
651 sys.exit(compare_read_families(sys.argv)) |