Mercurial > repos > scottx611x > qualimap2_bamqc

annotate qualimap_bamqc.py @ 40:98944e914637 draft

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planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
author scottx611x
date Fri, 27 Jul 2018 11:45:23 -0400
parents 2284e9b4c6b2
children e856fda6f375
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1 #!/usr/bin/env python
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2 from __future__ import print_function
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3 import argparse
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4 import os
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5 from subprocess import check_call, CalledProcessError
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6 import shutil
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7 import sys
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10 def qualimap_bamqc(bam_filename, genomecov_file, out_dir, jv_mem_size):
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11 qualimap_command = [
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12 "qualimap", "bamqc",
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13 "-bam " + bam_filename,
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14 "-oc " + genomecov_file,
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15 "-outdir " + out_dir,
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16 "--java-mem-size=" + jv_mem_size
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17 ]
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19 try:
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20 check_call(qualimap_command)
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21 except CalledProcessError:
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22 print("Error running the qualimap bamqc", file=sys.stderr)
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25 def main():
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26 parser = argparse.ArgumentParser(
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27 description="Generate Bam Quality Statistics"
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28 )
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29 parser.add_argument('--input_file')
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30 parser.add_argument('--out_genome_file')
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31 parser.add_argument('--out_dir')
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32 parser.add_argument('--java_mem_size')
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34 args = parser.parse_args()
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35 print(args)
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37 output_dir = os.path.dirname(args.out_genome_file)
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39 qualimap_bamqc(
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40 args.input_file,
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41 args.out_genome_file,
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42 args.out_dir,
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43 args.java_mem_size
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44 )
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46 shutil.make_archive(
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47 'raw_data_qualimapReport',
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48 'zip',
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49 args.out_dir + '/raw_data_qualimapReport'
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50 )
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52 shutil.move(
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53 "raw_data_qualimapReport.zip",
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54 os.path.join(output_dir, "raw_data_qualimapReport.zip")
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55 )
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57 [
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58 shutil.move(
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59 os.path.join(args.out_dir, file_name),
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60 os.path.join(output_dir, file_name)
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61 )
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62 for file_name in ["genome_results.txt", "qualimapReport.html"]
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63 ]
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65 if __name__ == "__main__":
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66 main()