# HG changeset patch # User artbio # Date 1539119697 14400 # Node ID 8ea06787c08af9689ff361d1a224418e9f1ba74e # Parent ae9ea0488850473fbd8b8fb192ed774e9634ce7c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079 diff -r ae9ea0488850 -r 8ea06787c08a bamparse.py --- a/bamparse.py Sun Oct 15 19:14:29 2017 -0400 +++ b/bamparse.py Tue Oct 09 17:14:57 2018 -0400 @@ -9,10 +9,6 @@ the_parser = argparse.ArgumentParser() the_parser.add_argument('--output', nargs='+', action='store', type=str, help='Count tables') - the_parser.add_argument('--polarity', - choices=["sense", "antisense", "both"], - help="forward, reverse or both forward an\ - reverse reads are counted") the_parser.add_argument('--alignments', nargs='+', help="bam alignments files") the_parser.add_argument('--labels', nargs='+', help="Alignments labels") @@ -23,37 +19,17 @@ return args -def get_counts(bamfile, polarity="both"): +def get_counts(bamfile): """ Takes an AlignmentFile object and returns a dictionary of counts for sense, - antisense, or both sense and antisense reads aligning to the bam references + antisense, or both sense and antisense bam alignments to the references, + depending on the pre-treatment performed by sambamba in the xml wrapper """ - def filter_sense_read(read): - if read.is_reverse: - return 0 - else: - return 1 - - def filter_antisense_read(read): - if read.is_reverse: - return 1 - else: - return 0 - counts = defaultdict(int) for ref_name in bamfile.references: counts[ref_name] = 0 - if polarity == "both": - for ref_name in bamfile.references: - counts[ref_name] = bamfile.count(reference=ref_name) - if polarity == "sense": - for ref_name in bamfile.references: - for read in bamfile.fetch(ref_name): - counts[ref_name] += filter_sense_read(read) - if polarity == "antisense": - for ref_name in bamfile.references: - for read in bamfile.fetch(ref_name): - counts[ref_name] += filter_antisense_read(read) + for ref_name in bamfile.references: + counts[ref_name] = bamfile.count(reference=ref_name) return counts @@ -80,14 +56,14 @@ out.close() -def main(alignments, labels, polarity, output, number): +def main(alignments, labels, output, number): diclist = [] for file in alignments: bam_object = pysam.AlignmentFile(file, 'rb') - diclist.append(get_counts(bam_object, polarity=polarity)) + diclist.append(get_counts(bam_object)) writetable(diclist, labels, output, number) if __name__ == "__main__": args = Parser() - main(args.alignments, args.labels, args.polarity, args.output, args.number) + main(args.alignments, args.labels, args.output, args.number) diff -r ae9ea0488850 -r 8ea06787c08a bamparse.xml --- a/bamparse.xml Sun Oct 15 19:14:29 2017 -0400 +++ b/bamparse.xml Tue Oct 09 17:14:57 2018 -0400 @@ -1,28 +1,34 @@ - + in a BAM file - bowtie - numpy pysam + sambamba @@ -44,6 +50,58 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + **What it does** @@ -56,20 +114,4 @@ The library labels in the returned count table are taken from the input bam datasets names in the Galaxy history. - - - - - - - - - - - - - - - - diff -r ae9ea0488850 -r 8ea06787c08a test-data/input1.bam Binary file test-data/input1.bam has changed diff -r ae9ea0488850 -r 8ea06787c08a test-data/input2.bam Binary file test-data/input2.bam has changed diff -r ae9ea0488850 -r 8ea06787c08a test-data/input_new2.bam Binary file test-data/input_new2.bam has changed diff -r ae9ea0488850 -r 8ea06787c08a test-data/more_antisense_table.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/more_antisense_table.tabular Tue Oct 09 17:14:57 2018 -0400 @@ -0,0 +1,31 @@ +gene input1.bam input2.bam input_new2.bam +FBtr0070001 0 0 0 +FBtr0070533 0 0 0 +FBtr0070603 0 0 0 +FBtr0070604 0 0 0 +FBtr0070911 0 0 0 +FBtr0078490 0 0 0 +FBtr0078580 0 0 0 +FBtr0078790 1 0 0 +FBtr0079064 0 0 0 +FBtr0079090 1 0 0 +FBtr0079338 0 0 0 +FBtr0079528 0 0 0 +FBtr0079596 0 1 1 +FBtr0079677 0 0 0 +FBtr0079690 0 0 0 +FBtr0079692 0 0 0 +FBtr0079693 0 0 0 +FBtr0079694 0 0 0 +FBtr0079702 0 0 0 +FBtr0079728 0 0 0 +FBtr0079729 0 0 0 +FBtr0079752 0 0 0 +FBtr0079820 0 0 0 +FBtr0080609 0 0 0 +FBtr0080644 0 0 0 +FBtr0080646 0 0 0 +FBtr0080647 0 0 0 +FBtr0080660 0 0 0 +FBtr0080663 0 0 0 +FBtr0080664 0 2 2 diff -r ae9ea0488850 -r 8ea06787c08a test-data/more_sense_table.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/more_sense_table.tabular Tue Oct 09 17:14:57 2018 -0400 @@ -0,0 +1,31 @@ +gene input1.bam input2.bam input_new2.bam +FBtr0070001 57 24 24 +FBtr0070533 24 45 45 +FBtr0070603 70 61 61 +FBtr0070604 40 55 55 +FBtr0070911 2 3 3 +FBtr0078490 8 14 14 +FBtr0078580 1104 370 370 +FBtr0078790 13 10 10 +FBtr0079064 4 5 0 +FBtr0079090 5 7 7 +FBtr0079338 16 23 23 +FBtr0079528 106 365 365 +FBtr0079596 152 315 315 +FBtr0079677 4 7 7 +FBtr0079690 5 5 5 +FBtr0079692 6 4 4 +FBtr0079693 6 9 9 +FBtr0079694 7 6 6 +FBtr0079702 4 4 4 +FBtr0079728 8 6 6 +FBtr0079729 4 4 4 +FBtr0079752 8 2 2 +FBtr0079820 13 109 109 +FBtr0080609 63 8 8 +FBtr0080644 6 8 8 +FBtr0080646 3 12 12 +FBtr0080647 10 12 12 +FBtr0080660 7 11 11 +FBtr0080663 115 106 106 +FBtr0080664 128 387 387 diff -r ae9ea0488850 -r 8ea06787c08a test-data/more_table0.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/more_table0.tabular Tue Oct 09 17:14:57 2018 -0400 @@ -0,0 +1,31 @@ +gene input1.bam +FBtr0070001 57 +FBtr0070533 24 +FBtr0070603 70 +FBtr0070604 40 +FBtr0070911 2 +FBtr0078490 8 +FBtr0078580 1104 +FBtr0078790 14 +FBtr0079064 4 +FBtr0079090 6 +FBtr0079338 16 +FBtr0079528 106 +FBtr0079596 152 +FBtr0079677 4 +FBtr0079690 5 +FBtr0079692 6 +FBtr0079693 6 +FBtr0079694 7 +FBtr0079702 4 +FBtr0079728 8 +FBtr0079729 4 +FBtr0079752 8 +FBtr0079820 13 +FBtr0080609 63 +FBtr0080644 6 +FBtr0080646 3 +FBtr0080647 10 +FBtr0080660 7 +FBtr0080663 115 +FBtr0080664 128 diff -r ae9ea0488850 -r 8ea06787c08a test-data/more_table1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/more_table1.tabular Tue Oct 09 17:14:57 2018 -0400 @@ -0,0 +1,31 @@ +gene input2.bam +FBtr0070001 24 +FBtr0070533 45 +FBtr0070603 61 +FBtr0070604 55 +FBtr0070911 3 +FBtr0078490 14 +FBtr0078580 370 +FBtr0078790 10 +FBtr0079064 5 +FBtr0079090 7 +FBtr0079338 23 +FBtr0079528 365 +FBtr0079596 316 +FBtr0079677 7 +FBtr0079690 5 +FBtr0079692 4 +FBtr0079693 9 +FBtr0079694 6 +FBtr0079702 4 +FBtr0079728 6 +FBtr0079729 4 +FBtr0079752 2 +FBtr0079820 109 +FBtr0080609 8 +FBtr0080644 8 +FBtr0080646 12 +FBtr0080647 12 +FBtr0080660 11 +FBtr0080663 106 +FBtr0080664 389 diff -r ae9ea0488850 -r 8ea06787c08a test-data/more_table2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/more_table2.tabular Tue Oct 09 17:14:57 2018 -0400 @@ -0,0 +1,31 @@ +gene input_new2.bam +FBtr0070001 24 +FBtr0070533 45 +FBtr0070603 61 +FBtr0070604 55 +FBtr0070911 3 +FBtr0078490 14 +FBtr0078580 370 +FBtr0078790 10 +FBtr0079064 0 +FBtr0079090 7 +FBtr0079338 23 +FBtr0079528 365 +FBtr0079596 316 +FBtr0079677 7 +FBtr0079690 5 +FBtr0079692 4 +FBtr0079693 9 +FBtr0079694 6 +FBtr0079702 4 +FBtr0079728 6 +FBtr0079729 4 +FBtr0079752 2 +FBtr0079820 109 +FBtr0080609 8 +FBtr0080644 8 +FBtr0080646 12 +FBtr0080647 12 +FBtr0080660 11 +FBtr0080663 106 +FBtr0080664 389 diff -r ae9ea0488850 -r 8ea06787c08a test-data/table_antisense.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/table_antisense.tabular Tue Oct 09 17:14:57 2018 -0400 @@ -0,0 +1,239 @@ +gene alignment1.bam alignment2.bam +dme-bantam 0 0 +dme-let-7 0 0 +dme-mir-1 0 0 +dme-mir-10 0 0 +dme-mir-100 0 0 +dme-mir-1000 0 0 +dme-mir-1001 0 0 +dme-mir-1002 0 0 +dme-mir-1003 0 0 +dme-mir-1004 0 0 +dme-mir-1005 0 0 +dme-mir-1006 0 0 +dme-mir-1007 0 0 +dme-mir-1008 0 0 +dme-mir-1009 0 0 +dme-mir-1010 0 0 +dme-mir-1011 0 0 +dme-mir-1012 0 0 +dme-mir-1013 0 0 +dme-mir-1014 0 0 +dme-mir-1015 0 0 +dme-mir-1016 0 0 +dme-mir-1017 0 0 +dme-mir-11 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