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annotate bamparse.py @ 0:2a1a2bc6ae8b draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
author artbio
date Fri, 13 Oct 2017 02:59:36 -0400
parents
children ae9ea0488850
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0
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
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1 #!/usr/bin/env python
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
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2 import argparse
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
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3 from collections import defaultdict
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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4
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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5 import pysam
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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6
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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7
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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8 def Parser():
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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9 the_parser = argparse.ArgumentParser()
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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10 the_parser.add_argument('--output', nargs='+', action='store', type=str,
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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11 help='Count tables')
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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12 the_parser.add_argument('--polarity',
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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13 choices=["sense", "antisense", "both"],
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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14 help="forward, reverse or both forward an\
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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15 reverse reads are counted")
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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16 the_parser.add_argument('--alignments', nargs='+',
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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17 help="bam alignments files")
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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18 the_parser.add_argument('--labels', nargs='+', help="Alignments labels")
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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19 the_parser.add_argument('--number',
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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20 choices=["unique", "multiple"],
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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21 help="output is a single table or multiple tables")
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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22 args = the_parser.parse_args()
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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23 return args
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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24
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2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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26 def get_counts(bamfile, polarity="both"):
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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27 """
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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28 Takes an AlignmentFile object and returns a dictionary of counts for sense,
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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29 antisense, or both sense and antisense reads aligning to the bam references
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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30 """
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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31 def filter_sense_read(read):
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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32 if read.is_reverse:
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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33 return 0
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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34 else:
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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35 return 1
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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36
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37 def filter_antisense_read(read):
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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38 if read.is_reverse:
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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39 return 1
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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40 else:
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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41 return 0
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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42
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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43 counts = defaultdict(int)
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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44 for ref_name in bamfile.references:
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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45 counts[ref_name] = 0
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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46 if polarity == "both":
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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47 for ref_name in bamfile.references:
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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48 counts[ref_name] = bamfile.count(reference=ref_name)
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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49 if polarity == "sense":
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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50 for ref_name in bamfile.references:
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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51 for read in bamfile.fetch(ref_name):
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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52 counts[ref_name] += filter_sense_read(read)
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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53 if polarity == "antisense":
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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54 for ref_name in bamfile.references:
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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55 for read in bamfile.fetch(ref_name):
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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56 counts[ref_name] += filter_antisense_read(read)
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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57 return counts
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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58
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59
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60 def writetable(diclist, labels, output, number):
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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61 ''' diclist is a list of count dictionnaries '''
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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62 countlists = []
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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63 for dic in diclist:
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64 counts = sorted(dic.items())
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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65 counts = [j for (i,j) in counts]
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66 countlists.append(counts)
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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67 if number == "unique":
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68 out = open("outputdir/table.tabular", "w")
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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69 out.write("gene\t%s\n" % "\t".join(labels))
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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70 for countline in zip(sorted(diclist[0]), *countlists):
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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71 line = [ str(i) for i in countline]
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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72 out.write("%s\n" % "\t".join(line))
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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73 out.close()
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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74 else:
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75 for i, (dic, label) in enumerate(zip(diclist, labels)):
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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76 out = open("outputdir/table" + str(i) + ".tabular", "w")
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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77 out.write("gene\t%s\n" % label)
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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78 for gene in sorted(dic):
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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79 out.write("%s\t%s\n" % (gene, dic[gene]))
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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80 out.close()
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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81
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82
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83
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84 def main(alignments, labels, polarity, output, number):
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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85 diclist = []
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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86 for file in alignments:
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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87 bam_object = pysam.AlignmentFile(file, 'rb')
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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88 diclist.append(get_counts(bam_object, polarity=polarity))
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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89 writetable(diclist, labels, output, number)
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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90
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91
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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parents:
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92 if __name__ == "__main__":
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
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93 args = Parser()
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
94 main(args.alignments, args.labels, args.polarity, args.output, args.number)