Changeset 26
- Timestamp:
- Aug 11, 2010, 4:04:52 PM (11 years ago)
- bzr:base-revision:
- j@dannynavarro.net-20100806113756-c05d2haeot4rmaiy
- bzr:committer:
- Danny Navarro <j@dannynavarro.net>
- bzr:file-ids:
mzcms/parsers.py parsers.py-20100806092910-g1sxvv1o5b9umkof-1- bzr:mapping-version:
- v4
- bzr:repository-uuid:
- 724254b2-fbe6-419d-9466-c04ef4c9d29d
- bzr:revision-id:
- j@dannynavarro.net-20100806120031-x0349ul02lytyb8h
- bzr:revno:
- 26
- bzr:revprop:branch-nick:
- trunk
- bzr:root:
- trunk
- bzr:timestamp:
- 2010-08-06 14:00:31.428999901 +0200
- bzr:user-agent:
- bzr2.1.2+bzr-svn1.0.3
- svn:original-date:
- 2010-08-06T12:00:31.429000Z
- File:
-
- 1 edited
Legend:
- Unmodified
- Added
- Removed
-
trunk/mzcms/parsers.py
r25 r26 3 3 """ 4 4 import sys 5 import os 5 6 import re 6 7 import csv … … 190 191 """Parses all the dat files in dats_dir 191 192 """ 192 dat s = get_dat_files(dats_dir)193 dat_paths = (f for f in os.walk(dats_dir)) 193 194 proteins = proteins_factory() 194 195 peptides = peptides_factory() … … 196 197 psms = psms_factory() 197 198 dat_parser = DatParser(decoy_str, scans_in_title) 198 for dat in dats: 199 dat_proteins, dat_peptides, dat_spectra, dat_psms = dat_parser.parse(file) 200 proteins.update(dat_proteins) 201 peptides.update(dat_peptides) 202 spectra.update(dat_spectra) 203 psms.update(dat_psms) 199 for dat_path in dat_paths: 200 with open(dat_path) as dat_file: 201 dat_proteins, dat_peptides, \ 202 dat_spectra, dat_psms = dat_parser.parse(dat_file) 203 proteins.update(dat_proteins) 204 peptides.update(dat_peptides) 205 spectra.update(dat_spectra) 206 psms.update(dat_psms) 204 207 return proteins, peptides, spectra, psms 205 208
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