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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit 73d041253a6c8d3f1126894c547e43dda5e700c1
author artbio
date Wed, 15 Jun 2022 15:36:40 +0000
parents 1e10a4538f3f
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1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
1 import argparse
1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
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2 from collections import defaultdict
1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
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1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
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4 import pysam
1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
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1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
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1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
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7 def Parser():
1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
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8 the_parser = argparse.ArgumentParser()
1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
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9 the_parser.add_argument('-bam', '--bam', dest='bam', required=True,
1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
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10 help='input BAM file')
1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
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11 the_parser.add_argument('-o', '--output', dest='distribution',
1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
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12 required=True,
1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
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13 help='tabular output for mapq distribution')
1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
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14 args = the_parser.parse_args()
1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
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15 return args
1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
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18 def collect_mapq(bam, out):
1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
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19 samfile = pysam.AlignmentFile(bam, "rb")
1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
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20 mapq_dict = defaultdict(int)
1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
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21 for read in samfile:
1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
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22 mapq_dict[read.mapping_quality] += 1
1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
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23 with open(out, 'w') as out:
1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
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24 out.write('mapq\tnumber_of_alignments\n')
1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
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25 for quality in sorted(mapq_dict):
1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
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26 out.write(f"{quality}\t{mapq_dict[quality]}\n")
1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
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27 return mapq_dict
1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
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30 def main(bam, out):
1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
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31 collect_mapq(bam, out)
1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
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34 if __name__ == "__main__":
1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
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35 args = Parser()
1e10a4538f3f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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36 main(args.bam, args.distribution)