Changeset 29

Timestamp:

Aug 11, 2010, 4:05:43 PM (11 years ago)

Author:

j@…

bzr:base-revision:

j@dannynavarro.net-20100806130525-yx7xmtqcmpfmxqrh

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-20100806131029-8dov1nqec1ao917u

bzr:revno:

29

bzr:revprop:branch-nick:

trunk

bzr:root:

trunk

bzr:timestamp:

2010-08-06 15:10:29.417999983 +0200

bzr:user-agent:

bzr2.1.2+bzr-svn1.0.3

svn:original-date:

2010-08-06T13:10:29.418000Z

Message:

handle ETD and CID fragmode from instrument type

File:

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

trunk/mzcms/parsers.py

@@ -51 +51 @@
         for line in datfile:
             if line.startswith("FILE="):
-                #XXX: There must be something in the standard library
-                # to normalize this properly
                 full_path = line.strip().split('=')[1]
-                norm_path = full_path.replace("\\", "/")
+                norm_path = full_path.replace('\\', '/')
                 return norm_path.split("/")[-1]
 
@@ -63 +61 @@
         for line in datfile:
             if line.startswith("INSTRUMENT="):
-                if line.strip().split('=')[1] == "ETD-TRAP":
+                frag_line = line.strip().split('=')[1]
+                if frag_line == "ETD-TRAP":
                     return 'ETD'
+                elif frag_line == "ESI-TRAP":
+                    return 'CID'
                 else:
-                    return 'CID'
+                    return frag_line
 
     def _parse_annotations(self, datfile):
@@ -143 +144 @@
         """Takes a dat file and returns a dictionary of psms.
         """
-        # TODO: handle frag_mode from mgf data
         pkl_fn = self._parse_spectra_fn(datfile)
         frag_mode = self._parse_frag_mode(datfile)