Mercurial > repos > rmarenco > hub_archive_creator
comparison hub-archive-creator-1.6/twoBitCreator.py @ 0:163b2de763ea draft
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| author | rmarenco |
|---|---|
| date | Tue, 01 Mar 2016 19:43:25 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:163b2de763ea |
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| 1 #!/usr/bin/python | |
| 2 | |
| 3 import os | |
| 4 import tempfile | |
| 5 import subprocess | |
| 6 | |
| 7 | |
| 8 def twoBitFileCreator(fastaFile, toolDirectory, mySpecieFolder): | |
| 9 """ | |
| 10 2bit file creator from a fasta file. | |
| 11 Need faTwoBit kentUtil. | |
| 12 Output a .2bit file | |
| 13 """ | |
| 14 baseNameFasta = os.path.basename(fastaFile.name) | |
| 15 suffixTwoBit, extensionTwoBit = os.path.splitext(baseNameFasta) | |
| 16 nameTwoBit = suffixTwoBit + '.2bit' | |
| 17 | |
| 18 with open(os.path.join(mySpecieFolder, nameTwoBit), 'w') as twoBitFile: | |
| 19 p = subprocess.Popen( | |
| 20 [os.path.join(toolDirectory, 'tools/faToTwoBit'), | |
| 21 fastaFile.name, | |
| 22 twoBitFile.name]) | |
| 23 | |
| 24 p.wait() | |
| 25 | |
| 26 return twoBitFile |