Mercurial > repos > cathywise > truststore_import
comparison TrustStoreGalaxyImport.py @ 23:cf4cf95e6678
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| author | Catherine Wise <catherine.wise@csiro.au> |
|---|---|
| date | Mon, 13 Jan 2014 09:21:20 +1100 |
| parents | 1179f6e90e78 |
| children | 7b1720b6acf2 |
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| 22:1179f6e90e78 | 23:cf4cf95e6678 |
|---|---|
| 63 print "File is compressed (gzip) but not valid." | 63 print "File is compressed (gzip) but not valid." |
| 64 sys.exit(4) | 64 sys.exit(4) |
| 65 elif is_gzipped and is_valid: | 65 elif is_gzipped and is_valid: |
| 66 # We need to uncompress the temp_name file, but BAM files must remain compressed in the BGZF format | 66 # We need to uncompress the temp_name file, but BAM files must remain compressed in the BGZF format |
| 67 CHUNK_SIZE = 2**20 # 1Mb | 67 CHUNK_SIZE = 2**20 # 1Mb |
| 68 fd, uncompressed = tempfile.mkstemp(prefix='data_id_%s_upload_gunzip_' % dataset.dataset_id, dir=os.path.dirname(outputFile), text=False ) | 68 fd, uncompressed = tempfile.mkstemp(prefix='data_id_upload_gunzip_', dir=os.path.dirname(outputFile), text=False ) |
| 69 gzipped_file = gzip.GzipFile(download, 'rb') | 69 gzipped_file = gzip.GzipFile(download, 'rb') |
| 70 while 1: | 70 while 1: |
| 71 try: | 71 try: |
| 72 chunk = gzipped_file.read(CHUNK_SIZE) | 72 chunk = gzipped_file.read(CHUNK_SIZE) |
| 73 except IOError: | 73 except IOError: |