fsd: fsd.py annotate

annotate fsd.py @ 17:2e517a54eedc draft

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

author	mheinzl
date	Tue, 02 Apr 2019 05:10:09 -0400
parents	6bd9ef49d013
children	c825a29a7d9f

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
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: 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 --output_tabular outptufile_name_tabular --output_pdf outptufile_name_pdf
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
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	18
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	19 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	20 import numpy
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	21 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	22
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	23 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	24
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 def readFileReferenceFree(file):
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	27 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	28 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	29 return(data_array)
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	30
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 def make_argparser():
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	33 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	34 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	35 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	36 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	37 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	38 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	39 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	40 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	41 parser.add_argument('--inputName4')
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('--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	43 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	44 return parser
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	45
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	46
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	47 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	48
16 6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	49 parser = make_argparser()
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	50 args = parser.parse_args(argv[1:])
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	51 firstFile = args.inputFile1
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	52 name1 = args.inputName1
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	53 secondFile = args.inputFile2
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	54 name2 = args.inputName2
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	55 thirdFile = args.inputFile3
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	56 name3 = args.inputName3
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	57 fourthFile = args.inputFile4
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	58 name4 = args.inputName4
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	59 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	60 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	61
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	62 sep = "\t"
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	63
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	64 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	65 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	66 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	67 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	68 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	69
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	70 list_to_plot = []
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	71 label = []
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	72 data_array_list = []
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	73 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	74 fig = plt.figure()
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	75 plt.subplots_adjust(bottom=0.25)
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	76 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	77 file1 = readFileReferenceFree(firstFile)
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	78 integers = numpy.array(file1[:, 0]).astype(int) # keep original family sizes
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	79
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	80 # for plot: replace all big family sizes by 22
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	81 data1 = numpy.array(file1[:, 0]).astype(int)
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	82 bigFamilies = numpy.where(data1 > 20)[0]
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	83 data1[bigFamilies] = 22
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	84
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	85 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	86 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	87 label.append(name1)
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	88 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	89
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	90 legend = "\n\n\n{}".format(name1)
17 2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	91 plt.text(0.05, 0.11, 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	92 legend1 = "singletons:\nnr. of tags\n{:,}".format(numpy.bincount(data1)[1])
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	93 plt.text(0.32, 0.11, 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	94
17 2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	95 legend3 = "freq. of tags\n{:.3f}".format(float(numpy.bincount(data1)[1]) / len(data1))
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	96 plt.text(0.41, 0.11, 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	97
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	98 legend3b = "PE reads\n{:.3f}".format(float(numpy.bincount(data1)[1]) / sum(integers))
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	99 plt.text(0.5, 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	100
17 2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	101 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))
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	102 plt.text(0.58, 0.11, legend4, 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	103
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	104 legend5 = "PE reads\n{:,} ({:.3f})".format(sum(integers[integers > 20]), float(sum(integers[integers > 20])) / sum(integers))
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	105 plt.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	106
17 2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	107 legend6 = "total nr. of\ntags\n{:,}".format(len(data1))
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	108 plt.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	109
17 2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	110 legend6b = "PE reads\n{:,}".format(sum(integers))
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	111 plt.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	112
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	113 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	114 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	115 integers2 = numpy.array(file2[:, 0]).astype(int) # keep original family sizes
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	116
16 6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	117 data2 = numpy.asarray(file2[:, 0]).astype(int)
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	118 bigFamilies2 = numpy.where(data2 > 20)[0]
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	119 data2[bigFamilies2] = 22
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	120
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	121 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	122 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	123 label.append(name2)
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	124 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	125
17 2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	126 plt.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	127
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	128 legend1 = "{:,}".format(numpy.bincount(data2)[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	129 plt.text(0.32, 0.09, 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	130
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	131 legend3 = "{:.3f}".format(float(numpy.bincount(data2)[1]) / len(data2))
17 2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	132 plt.text(0.41, 0.09, 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	133
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	134 legend3b = "{:.3f}".format(float(numpy.bincount(data2)[1]) / sum(integers2))
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	135 plt.text(0.5, 0.09, 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	136
17 2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	137 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	138 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	139 float(numpy.bincount(data2)[len(numpy.bincount(data2)) - 1]) / len(data2))
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	140 plt.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	141
17 2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	142 legend5 = "{:,} ({:.3f})".format(sum(integers2[integers2 > 20]), float(sum(integers2[integers2 > 20])) / sum(integers2))
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	143 plt.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	144
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	145 legend6 = "{:,}".format(len(data2))
17 2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	146 plt.text(0.82, 0.09, legend6, 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	147
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	148 legend6b = "{:,}".format(sum(integers2))
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	149 plt.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	150
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	151 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	152 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	153 integers3 = numpy.array(file3[:, 0]).astype(int) # keep original family sizes
16 6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	154
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	155 data3 = numpy.asarray(file3[:, 0]).astype(int)
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	156 bigFamilies3 = numpy.where(data3 > 20)[0]
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	157 data3[bigFamilies3] = 22
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	158
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	159 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	160 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	161 label.append(name3)
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	162 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	163
17 2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	164 plt.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	165
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	166 legend1 = "{:,}".format(numpy.bincount(data3)[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	167 plt.text(0.32, 0.07, 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	168
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	169 legend3 = "{:.3f}".format(float(numpy.bincount(data3)[1]) / len(data3))
17 2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	170 plt.text(0.41, 0.07, 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	171
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	172 legend3b = "{:.3f}".format(float(numpy.bincount(data3)[1]) / sum(integers3))
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	173 plt.text(0.5, 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	174
17 2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	175 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	176 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	177 float(numpy.bincount(data3)[len(numpy.bincount(data3)) - 1]) / len(data3))
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	178 plt.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	179
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 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	181 float(sum(integers3[integers3 > 20])) / sum(integers3))
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	182 plt.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	183
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	184 legend6 = "{:,}".format(len(data3))
17 2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	185 plt.text(0.82, 0.07, legend6, 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	186
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	187 legend6b = "{:,}".format(sum(integers3))
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	188 plt.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	189
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	190 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	191 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	192 integers4 = numpy.array(file4[:, 0]).astype(int) # keep original family sizes
16 6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	193
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	194 data4 = numpy.asarray(file4[:, 0]).astype(int)
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	195
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	196 bigFamilies4 = numpy.where(data4 > 20)[0]
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	197 data4[bigFamilies4] = 22
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	198
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	199 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	200 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	201 label.append(name4)
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	202 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	203
17 2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	204 plt.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	205
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	206 legend1 = "{:,}".format(numpy.bincount(data4)[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	207 plt.text(0.32, 0.05, 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	208
17 2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	209 legend3 = "{:.3f}".format(float(numpy.bincount(data4)[1]) / len(data4))
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	210 plt.text(0.41, 0.05, 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	211
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	212 legend3b = "{:.3f}".format(float(numpy.bincount(data4)[1]) / sum(integers4))
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	213 plt.text(0.5, 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	214
17 2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	215 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	216 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	217 float(numpy.bincount(data4)[len(numpy.bincount(data4)) - 1]) / len(data4))
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	218 plt.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	219
17 2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	220 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	221 float(sum(integers4[integers4 > 20])) / sum(integers4))
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	222 plt.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	223
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	224 legend6 = "{:,}".format(len(data4))
17 2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	225 plt.text(0.82, 0.05, legend6, 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	226
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	227 legend6b = "{:,}".format(sum(integers4))
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	228 plt.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	229
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	230 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	231 minimumX = numpy.amin(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	232
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	233 counts = plt.hist(list_to_plot, bins=range(minimumX, maximumX + 1), stacked=False, edgecolor="black",
17 2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	234 linewidth=1, label=label, align="left", rwidth=0.8, alpha=0.7)
16 6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	235
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	236 ticks = numpy.arange(minimumX - 1, maximumX, 1)
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	237 ticks1 = map(str, ticks)
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	238 ticks1[len(ticks1) - 1] = ">20"
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	239 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	240
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	241 plt.legend(loc='upper right', fontsize=14, frameon=True, bbox_to_anchor=(0.9, 1))
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	242 # plt.title("Family Size Distribution", fontsize=14)
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	243 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	244 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	245 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	246 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	247 pdf.savefig(fig)
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	248 plt.close()
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	249
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	250 # write data to CSV file
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	251 output_file.write("Values from family size distribution with all datasets\n")
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	252 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	253 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	254 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	255 # 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	256 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	257 j = 0
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	258 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	259 if fs == 21:
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	260 fs = ">20"
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	261 else:
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	262 fs = "={}".format(fs)
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	263 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	264 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	265 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	266 else:
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	267 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	268 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	269 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	270 j += 1
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	271 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	272 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	273 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	274 else:
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	275 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	276 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	277
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	278 # 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	279 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	280 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	281 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	282
17 2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	283 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	284 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	285 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	286 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	287 # 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	288 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	289 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	290
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	291 # 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	292 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	293 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	294
17 2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	295 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	296 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	297
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	298 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	299 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	300
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	301 # 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	302 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	303 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	304 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	305 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	306
16 6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	307 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	308 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	309 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	310 ba = data[ba]
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	311
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	312 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	313 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	314
16 6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	315 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	316 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	317
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	318 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	319
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	320 # 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	321 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	322 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	323 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	324 dataBA_FS3_o = dataBA_o[dataBA_o >= 3]
16 6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	325 ab_FS3 = ab[ab >= 3]
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	326 ba_FS3 = ba[ba >= 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	327 ab_FS3_o = ab_o[ab_o >= 3]
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	328 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	329
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	330 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	331 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	332 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	333
17 2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	334 # 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	335 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	336 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	337 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	338
17 2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	339 fig = plt.figure()
16 6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	340 plt.subplots_adjust(bottom=0.3)
17 2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	341 counts = plt.hist(list1, bins=range(minimumX, maximumX + 1), stacked=True, label=["duplex", "ab", "ba"],
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	342 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	343 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	344 # tick labels of x axis
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	345 ticks = numpy.arange(minimumX - 1, maximumX, 1)
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	346 ticks1 = map(str, ticks)
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	347 ticks1[len(ticks1) - 1] = ">20"
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	348 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	349 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	350 last = counts[0][2][len(counts[0][0]) - 1] # large families
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	351
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	352 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	353 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	354 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	355 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	356 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	357 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	358
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	359 # 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	360 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	361 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	362
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	363 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	364 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	365
17 2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	366 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	367 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	368
17 2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	369 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	370 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	371
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	372 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	373 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	374
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	375 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	376 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	377
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	378 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	379 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	380
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	381 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	382 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	383
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	384 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	385 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	386
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	387 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	388 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	389
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	390 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	391 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	392 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	393 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	394 (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	395 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	396
2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	397 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	398 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	399 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	400 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	401 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	402 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	403
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	404 pdf.savefig(fig)
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	405 plt.close()
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	406
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	407 # 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	408 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	409 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	410 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	411 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	412 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	413
17 2e517a54eedc planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty mheinzl parents: 16 diff changeset	414 output_file.write("{}singletons:{}{}{}family size > 20:\n".format(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	415 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	416 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	417 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	418 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	419
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	420 # 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	421 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	422 "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	423 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	424 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	425 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	426 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	427 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	428 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	429 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	430 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	431 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	432 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	433 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	434 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	435 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	436 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	437 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	438 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	439 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	440 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	441 (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	442 (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	443 # 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	444 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	445 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	446 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	447 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	448 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	449 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	450 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	451 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	452 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	453 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	454 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	455 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	456 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	457 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	458 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	459 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	460 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	461 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	462 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	463 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	464 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	465 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	466 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	467 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	468 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	469 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	470
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	471 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	472 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	473 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	474 if fs == 21:
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	475 fs = ">20"
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	476 else:
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	477 fs = "={}".format(fs)
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	478 ab1 = ab - dx
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	479 ba1 = ba - ab
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	480 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	481
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	482 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	483
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	484
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	485 if __name__ == '__main__':
6bd9ef49d013 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a mheinzl parents: diff changeset	486 sys.exit(compare_read_families(sys.argv))

Mercurial > repos > mheinzl > fsd

annotate fsd.py @ 17:2e517a54eedc draft