Mercurial > repos > weilong-guo > bs_seeker2

comparison BSseeker2/galaxy/bs_seeker2_wrapper.py @ 1:8b26adf64adc draft default tip

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V2.0.5
author weilong-guo
date Tue, 05 Nov 2013 01:55:39 -0500
parents e6df770c0e58
children
comparison
equal deleted inserted replaced
0:e6df770c0e58 1:8b26adf64adc
112 '--db' : os.path.join(args[ALIGN]['--db'], 112 '--db' : os.path.join(args[ALIGN]['--db'],
113 os.path.split( getopt(args[ALIGN],'-g', '--genome', None))[1] + 113 os.path.split( getopt(args[ALIGN],'-g', '--genome', None))[1] +
114 ('_rrbs_%s_%s' % (getopt(args[ALIGN], '-l', '--low', '40'), 114 ('_rrbs_%s_%s' % (getopt(args[ALIGN], '-l', '--low', '40'),
115 getopt(args[ALIGN], '-u', '--up', '500')) 115 getopt(args[ALIGN], '-u', '--up', '500'))
116 if len(set(['-r', '--rrbs']) & set(args[ALIGN])) > 0 else '') + 116 if len(set(['-r', '--rrbs']) & set(args[ALIGN])) > 0 else '') +
117
118 '_' + args[ALIGN]['--aligner']) 117 '_' + args[ALIGN]['--aligner'])
119 }) 118 })
120 run_prog(os.path.join(path_to_bs_seeker, 'bs_seeker2-call_methylation.py'), args[CALL_METHYLATION]) 119 run_prog(os.path.join(path_to_bs_seeker, 'bs_seeker2-call_methylation.py'), args[CALL_METHYLATION])
121 120
122 if tempdir: 121 if tempdir: