Mercurial > repos > scottx611x > qualimap2_bamqc

annotate qualimap_bamqc.py @ 36:0e6aeed62025 draft

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planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
author scottx611x
date Thu, 26 Jul 2018 16:57:57 -0400
parents a3e9c80894dd
children 407b6a65c867
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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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9 OUTPUT_DIR = "qualimap_results"
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12 def qualimap_bamqc(bam_filename, genomecov_file, out_dir, jv_mem_size):
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13 qualimap_command = [
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14 "qualimap", "bamqc",
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15 "-bam " + bam_filename,
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16 "-oc " + genomecov_file,
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17 "-outdir " + out_dir,
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18 "--java-mem-size=" + jv_mem_size
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19 ]
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21 try:
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22 check_call(qualimap_command)
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23 except CalledProcessError:
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24 print("Error running the qualimap bamqc", file=sys.stderr)
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27 def main():
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28 parser = argparse.ArgumentParser(
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29 description="Generate Bam Quality Statistics"
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30 )
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31 parser.add_argument('--input_file')
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32 parser.add_argument('--out_genome_file')
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33 parser.add_argument('--out_dir')
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34 parser.add_argument('--java_mem_size')
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36 args = parser.parse_args()
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38 qualimap_bamqc(
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39 args.input_file,
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40 args.out_genome_file,
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41 args.out_dir,
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42 args.java_mem_size
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43 )
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45 print(os.listdir(os.getcwd()))
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46 print(os.listdir(args.out_dir))
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48 shutil.move(args.out_dir + "/genome_results.txt", "./genome_results.txt")
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49 shutil.move(args.out_dir + "/qualimapReport.html", "./qualimapReport.html")
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50 shutil.make_archive(
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51 './raw_data_qualimapReport',
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52 'zip',
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53 args.out_dir + '/raw_data_qualimapReport'
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54 )
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56 print(os.listdir(os.getcwd()))
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57 print(os.listdir(args.out_dir))
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59 if __name__ == "__main__":
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60 main()