Changeset 56

Timestamp:

Aug 11, 2010, 4:13:29 PM (11 years ago)

Author:

j@…

bzr:base-revision:

j@dannynavarro.net-20100811081721-bl1459g8nbhl4e67

bzr:committer:

Danny Navarro <j@dannynavarro.net>

bzr:file-ids:

mzcms/models.py models.py-20100730084238-fjjwldiefr0w07zv-4
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-20100811085044-aij4496kvr2j04x6

bzr:revno:

56

bzr:revprop:branch-nick:

trunk

bzr:root:

trunk

bzr:timestamp:

2010-08-11 10:50:44.831000090 +0200

bzr:user-agent:

bzr2.1.2+bzr-svn1.0.3

svn:original-date:

2010-08-11T08:50:44.831000Z

Message:

Added update method for proteins folder

Location:

trunk/mzcms

Files:

• models.py (modified) (2 diffs)
• parsers.py (modified) (1 diff)

trunk/mzcms/models.py

@@ -11 +11 @@
     def __init__(self):
         super(Experiment, self).__init__()
+
+class Proteins(Folder):
+    """A protein container"""
+    def update(self, protein_container):
+        """Updates the protein container so that if the protein is
+           already in the container only the peptide references are
+           added.
+        """
+        for prot_id, prot in protein_container.items():
+            if prot_id in self:
+                self[prot_id].pep_refs.extend(prot.pep_refs)
+            else:
+                self[prot_id] = prot
+
 
 class Protein(Persistent):
@@ -49 +63 @@
     if not 'app_root' in zodb_root:
         app_root = Experiment()
-        proteins = Folder()
+        proteins = Proteins()
         peptides = Folder()
         spectra = Folder()
+        psms = Folder()
         zodb_root['app_root'] = app_root
         app_root['proteins'] = proteins
         app_root['peptides'] = peptides
         app_root['spectra'] = spectra
-        psms = Folder()
         app_root['psms'] = psms
         folders = parse_dats('./dats',

trunk/mzcms/parsers.py

@@ -283 +283 @@
                     ser_proteins, ser_peptides, \
                     ser_spectra, ser_psms = dat_parser.parse(dat_file)
-                    for prot_id, prot in ser_proteins.items():
-                        if prot_id not in proteins:
-                            proteins[str(prot_id)] = prot
+                    proteins.update(ser_proteins)
                     transaction.savepoint()
                     for pep_id, pep in ser_peptides.items():