Mercurial > repos > iuc > transtermhp
comparison transtermhp.py @ 4:9a90656a1af9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
| author | iuc |
|---|---|
| date | Tue, 30 Oct 2018 20:25:05 -0400 |
| parents | 1a1ec22a7e28 |
| children |
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| 3:1a1ec22a7e28 | 4:9a90656a1af9 |
|---|---|
| 32 | 32 |
| 33 cmd = ['transterm', '-p', expterm, fasta, 'tmp.coords'] | 33 cmd = ['transterm', '-p', expterm, fasta, 'tmp.coords'] |
| 34 output = subprocess.check_output(cmd) | 34 output = subprocess.check_output(cmd) |
| 35 # TERM 1 4342 - 4366 + F 93 -11.5 -3.22878 | opp_overlap 4342, overlap 4340 4357 | 35 # TERM 1 4342 - 4366 + F 93 -11.5 -3.22878 | opp_overlap 4342, overlap 4340 4357 |
| 36 ttre = re.compile( | 36 ttre = re.compile( |
| 37 '^ (?P<name>.*) (?P<start>\d+) - (?P<end>\d+)\s+' | 37 r'^ (?P<name>.*) (?P<start>\d+) - (?P<end>\d+)\s+' |
| 38 '(?P<strand>[-+])\s+(?P<loc>[GFRTHNgfr]+)\s+' | 38 r'(?P<strand>[-+])\s+(?P<loc>[GFRTHNgfr]+)\s+' |
| 39 '(?P<conf>\d+)\s+(?P<hp>[0-9.-]+)\s+(?P<tail>[0-9.-]+)' | 39 r'(?P<conf>\d+)\s+(?P<hp>[0-9.-]+)\s+(?P<tail>[0-9.-]+)' |
| 40 ) | 40 ) |
| 41 | 41 |
| 42 rec.features = [] | 42 rec.features = [] |
| 43 batches = output.split('SEQUENCE ') | 43 batches = output.split('SEQUENCE ') |
| 44 for batch in batches[1:]: | 44 for batch in batches[1:]: |