Mercurial > repos > charles_s_test > seqsero2

comparison run_seqsero.py @ 10:53efef402c51 draft

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planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
author charles_s_test
date Wed, 29 Nov 2017 08:34:19 -0500
parents acc5cd06a36a
children
comparison
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9:acc5cd06a36a 10:53efef402c51
94 ''' 94 '''
95 outputs = [] 95 outputs = []
96 for run in run2fastqs: 96 for run in run2fastqs:
97 seqsero_cmd = [] 97 seqsero_cmd = []
98 if len(run2fastqs[run]) == 2: 98 if len(run2fastqs[run]) == 2:
99 seqsero_cmd = ['python', seqsero, '-m', '2', '-i', run2fastqs[run][0], run2fastqs[run][1]] 99 seqsero_cmd = ['python2.7', seqsero, '-m', '2', '-i', run2fastqs[run][0], run2fastqs[run][1]]
100 elif len(run2fastqs[run]) == 1: 100 elif len(run2fastqs[run]) == 1:
101 seqsero_cmd = ['python', seqsero, '-m', '1', '-i', run2fastqs[run][0]] 101 seqsero_cmd = ['python2,7', seqsero, '-m', '1', '-i', run2fastqs[run][0]]
102 p = Popen(seqsero_cmd, stdout=PIPE) 102 p = Popen(seqsero_cmd, stdout=PIPE)
103 output = p.communicate() 103 output = p.communicate()
104 outputs.append(output) 104 outputs.append(output)
105 return outputs 105 return outputs
106 106