Changeset 26

Timestamp:

Aug 11, 2010, 4:04:52 PM (11 years ago)

Author:

j@…

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

Message:

implemented dat path walker

File:

• trunk/mzcms/parsers.py (modified) (3 diffs)

trunk/mzcms/parsers.py

@@ -3 +3 @@
 """
 import sys
+import os
 import re
 import csv
@@ -190 +191 @@
     """Parses all the dat files in dats_dir
     """
-    dats = get_dat_files(dats_dir)
+    dat_paths = (f for f in os.walk(dats_dir))
     proteins = proteins_factory()
     peptides = peptides_factory()
@@ -196 +197 @@
     psms = psms_factory()
     dat_parser = DatParser(decoy_str, scans_in_title)
-    for dat in dats:
-        dat_proteins, dat_peptides, dat_spectra, dat_psms = dat_parser.parse(file)
-        proteins.update(dat_proteins)
-        peptides.update(dat_peptides)
-        spectra.update(dat_spectra)
-        psms.update(dat_psms)
+    for dat_path in dat_paths:
+        with open(dat_path) as dat_file:
+            dat_proteins, dat_peptides, \
+            dat_spectra, dat_psms = dat_parser.parse(dat_file)
+            proteins.update(dat_proteins)
+            peptides.update(dat_peptides)
+            spectra.update(dat_spectra)
+            psms.update(dat_psms)
     return proteins, peptides, spectra, psms