Mercurial > repos > sanbi-uwc > qualimap2
comparison qualimap_bamqc.py @ 5:465131fb4ce9 draft
planemo upload for repository https://github.com/zipho/qualimap2 commit 5a0a3d24e87ed5d8d027c1c5ecae6f5cd7b1f64d
| author | sanbi-uwc |
|---|---|
| date | Tue, 05 Apr 2016 03:53:28 -0400 |
| parents | a19abfa30ca7 |
| children |
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| 4:a19abfa30ca7 | 5:465131fb4ce9 |
|---|---|
| 8 | 8 |
| 9 log = logging.getLogger(__name__) | 9 log = logging.getLogger(__name__) |
| 10 | 10 |
| 11 | 11 |
| 12 def qualimap_bamqc(bam_filename, genomecov_file, out_dir, jv_mem_size): | 12 def qualimap_bamqc(bam_filename, genomecov_file, out_dir, jv_mem_size): |
| 13 cmdline_str = "qualimap bamqc -bam {} -oc {} -outdir {} --outfile {} --java-mem-size={}".format(bam_filename, | 13 cmdline_str = "qualimap bamqc -bam {} -oc {} -outdir {} --java-mem-size={}".format(bam_filename, |
| 14 genomecov_file, | 14 genomecov_file, |
| 15 out_dir, | 15 out_dir, |
| 16 jv_mem_size) | 16 jv_mem_size) |
| 17 cmdline = new_split(cmdline_str) | 17 cmdline = new_split(cmdline_str) |
| 18 try: | 18 try: |
| 19 check_call(cmdline) | 19 check_call(cmdline) |
| 20 except CalledProcessError: | 20 except CalledProcessError: |
| 21 print("Error running the qualimap bamqc", file=sys.stderr) | 21 print("Error running the qualimap bamqc", file=sys.stderr) |