Mercurial > repos > trinity_ctat > align_and_estimate_abundance
comparison trinityToolWrapper.py @ 4:cb71c6b0bf66 draft
Fix another python syntax error.
| author | trinity_ctat |
|---|---|
| date | Tue, 26 Sep 2017 11:48:19 -0400 |
| parents | 32b6a47c9312 |
| children | 98d99fed9d35 |
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| 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 |