Changeset 56
- Timestamp:
- Aug 11, 2010, 4:13:29 PM (11 years ago)
- 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
- Location:
- trunk/mzcms
- Files:
-
- 2 edited
Legend:
- Unmodified
- Added
- Removed
-
trunk/mzcms/models.py
r54 r56 11 11 def __init__(self): 12 12 super(Experiment, self).__init__() 13 14 class Proteins(Folder): 15 """A protein container""" 16 def update(self, protein_container): 17 """Updates the protein container so that if the protein is 18 already in the container only the peptide references are 19 added. 20 """ 21 for prot_id, prot in protein_container.items(): 22 if prot_id in self: 23 self[prot_id].pep_refs.extend(prot.pep_refs) 24 else: 25 self[prot_id] = prot 26 13 27 14 28 class Protein(Persistent): … … 49 63 if not 'app_root' in zodb_root: 50 64 app_root = Experiment() 51 proteins = Folder()65 proteins = Proteins() 52 66 peptides = Folder() 53 67 spectra = Folder() 68 psms = Folder() 54 69 zodb_root['app_root'] = app_root 55 70 app_root['proteins'] = proteins 56 71 app_root['peptides'] = peptides 57 72 app_root['spectra'] = spectra 58 psms = Folder()59 73 app_root['psms'] = psms 60 74 folders = parse_dats('./dats', -
trunk/mzcms/parsers.py
r55 r56 283 283 ser_proteins, ser_peptides, \ 284 284 ser_spectra, ser_psms = dat_parser.parse(dat_file) 285 for prot_id, prot in ser_proteins.items(): 286 if prot_id not in proteins: 287 proteins[str(prot_id)] = prot 285 proteins.update(ser_proteins) 288 286 transaction.savepoint() 289 287 for pep_id, pep in ser_peptides.items():
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