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annotate fsd_regions.py @ 11:37db9decb5d0 draft

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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
author mheinzl
date Mon, 26 Nov 2018 04:51:11 -0500
parents eabfdc012d7b
children 63432e6f6a61
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37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
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1 #!/usr/bin/env python
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
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2
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
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3 # Family size distribution of tags which were aligned to the reference genome
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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4 #
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5 # Author: Monika Heinzl & Gundula Povysil, Johannes-Kepler University Linz (Austria)
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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6 # Contact: monika.heinzl@edumail.at
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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7 #
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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8 # Takes at least one TABULAR file with tags before the alignment to the SSCS,
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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9 # a BAM file with tags of reads that overlap the regions of the reference genome and
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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10 # an optional BED file with chromosome, start and stop position of the regions as input.
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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11 # The program produces a plot which shows the distribution of family sizes of the tags from the input files and
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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12 # a tabular file with the data of the plot.
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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13
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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14 # USAGE: python FSD_regions.py --inputFile filenameSSCS --inputName1 filenameSSCS
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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15 # --bamFile DCSbamFile --rangesFile BEDfile --output_tabular outptufile_name_tabular
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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16 # --output_pdf outputfile_name_pdf
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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18 import argparse
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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19 import collections
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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20 import re
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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21 import sys
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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22
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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23 import matplotlib.pyplot as plt
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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24 import numpy as np
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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25 import pysam
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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26 from matplotlib.backends.backend_pdf import PdfPages
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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28 plt.switch_backend('agg')
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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31 def readFileReferenceFree(file, delim):
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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32 with open(file, 'r') as dest_f:
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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33 data_array = np.genfromtxt(dest_f, skip_header=0, delimiter=delim, comments='#', dtype='string')
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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34 return(data_array)
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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37 def make_argparser():
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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38 parser = argparse.ArgumentParser(description='Family Size Distribution of tags which were aligned to regions of the reference genome')
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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39 parser.add_argument('--inputFile', help='Tabular File with three columns: ab or ba, tag and family size.')
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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40 parser.add_argument('--inputName1')
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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41 parser.add_argument('--bamFile', help='BAM file with aligned reads.')
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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42 parser.add_argument('--rangesFile', default=None, help='BED file with chromosome, start and stop positions.')
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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43 parser.add_argument('--output_pdf', default="data.pdf", type=str, help='Name of the pdf and tabular file.')
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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44 parser.add_argument('--output_tabular', default="data.tabular", type=str, help='Name of the pdf and tabular file.')
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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45 return parser
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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47
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48 def compare_read_families_refGenome(argv):
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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49 parser = make_argparser()
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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50 args = parser.parse_args(argv[1:])
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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51
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52 firstFile = args.inputFile
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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53 name1 = args.inputName1
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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54 name1 = name1.split(".tabular")[0]
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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55 bamFile = args.bamFile
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56
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57 rangesFile = args.rangesFile
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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58 title_file = args.output_pdf
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59 title_file2 = args.output_tabular
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60 sep = "\t"
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61
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62 with open(title_file2, "w") as output_file, PdfPages(title_file) as pdf:
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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63 data_array = readFileReferenceFree(firstFile, "\t")
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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64 pysam.index(bamFile)
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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65
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66 bam = pysam.AlignmentFile(bamFile, "rb")
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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67 qname_dict = collections.OrderedDict()
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68
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69 if rangesFile != str(None):
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70 with open(rangesFile, 'r') as regs:
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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71 range_array = np.genfromtxt(regs, skip_header=0, delimiter='\t', comments='#', dtype='string')
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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72
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73 if range_array.ndim == 0:
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74 print("Error: file has 0 lines")
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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75 exit(2)
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76
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77 if range_array.ndim == 1:
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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78 chrList = range_array[0]
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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79 start_posList = range_array[1].astype(int)
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
80 stop_posList = range_array[2].astype(int)
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
81 chrList = [chrList.tolist()]
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
82 start_posList = [start_posList.tolist()]
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
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diff changeset
83 stop_posList = [stop_posList.tolist()]
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
84 else:
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
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diff changeset
85 chrList = range_array[:, 0]
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
86 start_posList = range_array[:, 1].astype(int)
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
87 stop_posList = range_array[:, 2].astype(int)
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
88
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
89 if len(start_posList) != len(stop_posList):
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
90 print("start_positions and end_positions do not have the same length")
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
91 exit(3)
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
92
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
93 chrList = np.array(chrList)
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
94 start_posList = np.array(start_posList).astype(int)
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
95 stop_posList = np.array(stop_posList).astype(int)
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
96 for chr, start_pos, stop_pos in zip(chrList, start_posList, stop_posList):
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
97 chr_start_stop = "{}_{}_{}".format(chr, start_pos, stop_pos)
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
98 qname_dict[chr_start_stop] = []
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
99 for read in bam.fetch(chr.tobytes(), start_pos, stop_pos):
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
100 if not read.is_unmapped:
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
101 if re.search('_', read.query_name):
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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102 tags = re.split('_', read.query_name)[0]
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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103 else:
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104 tags = read.query_name
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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105 qname_dict[chr_start_stop].append(tags)
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
106
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diff changeset
107 else:
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
108 for read in bam.fetch():
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
109 if not read.is_unmapped:
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
110 if re.search(r'_', read.query_name):
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
111 tags = re.split('_', read.query_name)[0]
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
112 else:
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
113 tags = read.query_name
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diff changeset
114
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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115 if read.reference_name not in qname_dict.keys():
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
116 qname_dict[read.reference_name] = [tags]
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
117 else:
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
118 qname_dict[read.reference_name].append(tags)
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
119
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diff changeset
120 seq = np.array(data_array[:, 1])
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
121 tags = np.array(data_array[:, 2])
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
122 quant = np.array(data_array[:, 0]).astype(int)
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
123 group = np.array(qname_dict.keys())
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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124
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
125 all_ab = seq[np.where(tags == "ab")[0]]
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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126 all_ba = seq[np.where(tags == "ba")[0]]
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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127 quant_ab = quant[np.where(tags == "ab")[0]]
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
128 quant_ba = quant[np.where(tags == "ba")[0]]
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diff changeset
129
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diff changeset
130 seqDic_ab = dict(zip(all_ab, quant_ab))
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
131 seqDic_ba = dict(zip(all_ba, quant_ba))
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132
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diff changeset
133 lst_ab = []
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diff changeset
134 lst_ba = []
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diff changeset
135 quantAfterRegion = []
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diff changeset
136 length_regions = 0
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diff changeset
137 for i in group:
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diff changeset
138 lst_ab_r = []
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diff changeset
139 lst_ba_r = []
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
140 seq_mut = qname_dict[i]
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
141 if rangesFile == str(None):
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
142 seq_mut, seqMut_index = np.unique(np.array(seq_mut), return_index=True)
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
143 length_regions = length_regions + len(seq_mut) * 2
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
144 for r in seq_mut:
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
145 count_ab = seqDic_ab.get(r)
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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diff changeset
146 count_ba = seqDic_ba.get(r)
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diff changeset
147 lst_ab_r.append(count_ab)
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diff changeset
148 lst_ab.append(count_ab)
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diff changeset
149 lst_ba_r.append(count_ba)
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diff changeset
150 lst_ba.append(count_ba)
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diff changeset
151
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diff changeset
152 dataAB = np.array(lst_ab_r)
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diff changeset
153 dataBA = np.array(lst_ba_r)
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diff changeset
154 bigFamilies = np.where(dataAB > 20)[0]
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diff changeset
155 dataAB[bigFamilies] = 22
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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156 bigFamilies = np.where(dataBA > 20)[0]
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diff changeset
157 dataBA[bigFamilies] = 22
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diff changeset
158
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diff changeset
159 quantAll = np.concatenate((dataAB, dataBA))
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160 quantAfterRegion.append(quantAll)
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161
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162 quant_ab = np.array(lst_ab)
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163 quant_ba = np.array(lst_ba)
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164
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165 maximumX = np.amax(np.concatenate(quantAfterRegion))
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166 minimumX = np.amin(np.concatenate(quantAfterRegion))
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167
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168 # PLOT
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169 plt.rc('figure', figsize=(11.69, 8.27)) # A4 format
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170 plt.rcParams['axes.facecolor'] = "E0E0E0" # grey background color
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171 plt.rcParams['xtick.labelsize'] = 14
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172 plt.rcParams['ytick.labelsize'] = 14
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173 plt.rcParams['patch.edgecolor'] = "black"
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174 fig = plt.figure()
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175 plt.subplots_adjust(bottom=0.3)
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176
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177 colors = ["#6E6E6E", "#0431B4", "#5FB404", "#B40431", "#F4FA58", "#DF7401", "#81DAF5"]
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178
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179 col = []
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180 for i in range(0, len(group)):
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181 col.append(colors[i])
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182
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183 counts = plt.hist(quantAfterRegion, bins=range(minimumX, maximumX + 1), stacked=False, label=group,
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184 align="left", alpha=1, color=col, edgecolor="black", linewidth=1)
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185 ticks = np.arange(minimumX - 1, maximumX, 1)
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186
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187 ticks1 = map(str, ticks)
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188 ticks1[len(ticks1) - 1] = ">20"
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189 plt.xticks(np.array(ticks), ticks1)
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190 count = np.bincount(map(int, quant_ab)) # original counts
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191
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192 legend = "max. family size:\nabsolute frequency:\nrelative frequency:\n\ntotal nr. of reads:\n(before SSCS building)"
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193 plt.text(0.15, 0.085, legend, size=11, transform=plt.gcf().transFigure)
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194
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195 legend = "AB\n{}\n{}\n{:.5f}\n\n{:,}".format(max(map(int, quant_ab)), count[len(count) - 1], float(count[len(count) - 1]) / sum(count), sum(np.array(data_array[:, 0]).astype(int)))
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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196 plt.text(0.35, 0.105, legend, size=11, transform=plt.gcf().transFigure)
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197
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198 count2 = np.bincount(map(int, quant_ba)) # original counts
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199
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200 legend = "BA\n{}\n{}\n{:.5f}" \
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201 .format(max(map(int, quant_ba)), count2[len(count2) - 1], float(count2[len(count2) - 1]) / sum(count2))
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202 plt.text(0.45, 0.1475, legend, size=11, transform=plt.gcf().transFigure)
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203
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204 plt.text(0.55, 0.2125, "total nr. of tags:", size=11, transform=plt.gcf().transFigure)
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205 plt.text(0.8, 0.2125, "{:,} ({:,})".format(length_regions, length_regions / 2), size=11,
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206 transform=plt.gcf().transFigure)
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207
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208 legend4 = "* In the plot, both family sizes of the ab and ba strands were used.\nWhereas the total numbers indicate only the single count of the tags per region.\n"
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209 plt.text(0.1, 0.01, legend4, size=11, transform=plt.gcf().transFigure)
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210
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211 space = 0
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212 for i, count in zip(group, quantAfterRegion):
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213 plt.text(0.55, 0.15 - space, "{}:\n".format(i), size=11, transform=plt.gcf().transFigure)
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214 plt.text(0.8, 0.15 - space, "{:,}\n".format(len(count) / 2), size=11, transform=plt.gcf().transFigure)
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215 space = space + 0.02
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216
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217 plt.legend(loc='upper right', fontsize=14, bbox_to_anchor=(0.9, 1), frameon=True)
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218 plt.xlabel("Family size", fontsize=14)
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219 plt.ylabel("Absolute Frequency", fontsize=14)
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220 plt.grid(b=True, which="major", color="#424242", linestyle=":")
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221 plt.margins(0.01, None)
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222
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223 pdf.savefig(fig, bbox_inch="tight")
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224 plt.close()
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225
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226 output_file.write("Dataset:{}{}\n".format(sep, name1))
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227 output_file.write("{}AB{}BA\n".format(sep, sep))
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228 output_file.write("max. family size:{}{}{}{}\n".format(sep, max(map(int, quant_ab)), sep, max(map(int, quant_ba))))
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229 output_file.write("absolute frequency:{}{}{}{}\n".format(sep, count[len(count) - 1], sep, count2[len(count2) - 1]))
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230 output_file.write("relative frequency:{}{:.3f}{}{:.3f}\n\n".format(sep, float(count[len(count) - 1]) / sum(count), sep, float(count2[len(count2) - 1]) / sum(count2)))
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
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231 output_file.write("total nr. of reads{}{}\n".format(sep, sum(np.array(data_array[:, 0]).astype(int))))
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232 output_file.write("total nr. of tags{}{} ({})\n".format(sep, length_regions, length_regions / 2))
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233 output_file.write("\n\nValues from family size distribution\n")
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234 output_file.write("{}".format(sep))
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235 for i in group:
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diff changeset
236 output_file.write("{}{}".format(i, sep))
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
diff changeset
237 output_file.write("\n")
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
diff changeset
238
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
diff changeset
239 j = 0
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
diff changeset
240 for fs in counts[1][0:len(counts[1]) - 1]:
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
diff changeset
241 if fs == 21:
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
diff changeset
242 fs = ">20"
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
diff changeset
243 else:
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
diff changeset
244 fs = "={}".format(fs)
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
diff changeset
245 output_file.write("FS{}{}".format(fs, sep))
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
diff changeset
246 if len(group) == 1:
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
diff changeset
247 output_file.write("{}{}".format(int(counts[0][j]), sep))
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
diff changeset
248 else:
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
diff changeset
249 for n in range(len(group)):
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
diff changeset
250 output_file.write("{}{}".format(int(counts[0][n][j]), sep))
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
diff changeset
251 output_file.write("\n")
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
diff changeset
252 j += 1
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
diff changeset
253 output_file.write("sum{}".format(sep))
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
diff changeset
254
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
diff changeset
255 if len(group) == 1:
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
diff changeset
256 output_file.write("{}{}".format(int(sum(counts[0])), sep))
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
diff changeset
257 else:
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
diff changeset
258 for i in counts[0]:
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
diff changeset
259 output_file.write("{}{}".format(int(sum(i)), sep))
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
diff changeset
260 output_file.write("\n")
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
diff changeset
261 output_file.write("\n\nIn the plot, both family sizes of the ab and ba strands were used.\nWhereas the total numbers indicate only the single count of the tags per region.\n")
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
diff changeset
262 output_file.write("Region{}total nr. of tags per region\n".format(sep))
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
diff changeset
263 for i, count in zip(group, quantAfterRegion):
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
diff changeset
264 output_file.write("{}{}{}\n".format(i, sep, len(count) / 2))
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
diff changeset
265
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
diff changeset
266 print("Files successfully created!")
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
diff changeset
267
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
diff changeset
268
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
diff changeset
269 if __name__ == '__main__':
37db9decb5d0 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit 2aea9e30f5ed4fd3db3fb44ddb8aacb48a62eccc
mheinzl
parents: 9
diff changeset
270 sys.exit(compare_read_families_refGenome(sys.argv))