Mercurial > repos > mzeidler > virana2
comparison vref.py @ 1:3eddea30be1a draft
Uploaded fixed vref for ftputil version > 2.3
| author | mzeidler |
|---|---|
| date | Tue, 24 Sep 2013 10:41:55 -0400 |
| parents | 3ba5983012cf |
| children |
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| 0:3ba5983012cf | 1:3eddea30be1a |
|---|---|
| 325 | 325 |
| 326 def _get_nc(self, entry_path): | 326 def _get_nc(self, entry_path): |
| 327 | 327 |
| 328 if self.host.path.isfile(entry_path): | 328 if self.host.path.isfile(entry_path): |
| 329 logging.debug('Processing refseq entry %s' % entry_path) | 329 logging.debug('Processing refseq entry %s' % entry_path) |
| 330 remote_handle = self.host.file(entry_path) | 330 with self.host.file(entry_path) as remote_handle: |
| 331 | 331 |
| 332 | 332 |
| 333 for record, project, taxonomy, family, organism, gi\ | 333 for record, project, taxonomy, family, organism, gi\ |
| 334 in self._parse_genbank_records(remote_handle): | 334 in self._parse_genbank_records(remote_handle): |
| 335 | 335 |
| 336 cleaned = self._get_fasta_record(record, self.group , family, organism, gi) | 336 cleaned = self._get_fasta_record(record, self.group , family, organism, gi) |
| 337 | 337 |
| 338 yield cleaned | 338 yield cleaned |
| 339 | 339 |
| 340 def _get_nz(self, entry_path): | 340 def _get_nz(self, entry_path): |
| 341 | 341 |
| 342 scaffold_path = entry_path.replace('.gbk', '.scaffold.gbk.tgz') | 342 scaffold_path = entry_path.replace('.gbk', '.scaffold.gbk.tgz') |
| 343 if self.host.path.isfile(scaffold_path): | 343 if self.host.path.isfile(scaffold_path): |