Mercurial > repos > iuc > transtermhp

comparison transtermhp.py @ 4:9a90656a1af9 draft

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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
comparison
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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:]: