Mercurial > repos > trinity_ctat > align_and_estimate_abundance

comparison trinityToolWrapper.py @ 4:cb71c6b0bf66 draft

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Fix another python syntax error.
author trinity_ctat
date Tue, 26 Sep 2017 11:48:19 -0400
parents 32b6a47c9312
children 98d99fed9d35
comparison
equal deleted inserted replaced
3:32b6a47c9312 4:cb71c6b0bf66
30 else: 30 else:
31 TrinityPath, err_info = pipe1.communicate() 31 TrinityPath, err_info = pipe1.communicate()
32 # FIX - probably should be checking err_info for errors... 32 # FIX - probably should be checking err_info for errors...
33 # Determine the TRINITY_BASE_DIR from output1. 33 # Determine the TRINITY_BASE_DIR from output1.
34 # If TrinityPath is a link, we need to dereference the link. 34 # If TrinityPath is a link, we need to dereference the link.
35 while os.path.islink(TrinityPath) 35 while os.path.islink(TrinityPath):
36 TrinityPath = os.path.join(os.path.dirname(TrinityPath),os.readlink(TrinityPath)) 36 TrinityPath = os.path.join(os.path.dirname(TrinityPath),os.readlink(TrinityPath))
37 # Take off the last part of the path (which is the Trinity command) 37 # Take off the last part of the path (which is the Trinity command)
38 TRINITY_BASE_DIR = "/".join(TrinityPath.split("/")[0:-1]) 38 TRINITY_BASE_DIR = "/".join(TrinityPath.split("/")[0:-1])
39 39
40 # get bindir 40 # get bindir