Changeset 45
- Timestamp:
- Aug 11, 2010, 4:10:19 PM (11 years ago)
- bzr:base-revision:
- j@dannynavarro.net-20100809141712-f1elceltr5n95752
- 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-20100809152143-wupx7dm9da51912j
- bzr:revno:
- 45
- bzr:revprop:branch-nick:
- trunk
- bzr:root:
- trunk
- bzr:timestamp:
- 2010-08-09 17:21:43.714999914 +0200
- bzr:user-agent:
- bzr2.1.2+bzr-svn1.0.3
- svn:original-date:
- 2010-08-09T15:21:43.715000Z
- Location:
- trunk/mzcms
- Files:
-
- 2 edited
Legend:
- Unmodified
- Added
- Removed
-
trunk/mzcms/models.py
r44 r45 48 48 def __init__(self, scan, run, peaks, prec_mz, prec_charge): 49 49 self.scan = int(scan) 50 self.run = str( scan)50 self.run = str(run) 51 51 self.peaks = tuple(peaks) 52 52 self.prec_mz = float(prec_mz) -
trunk/mzcms/parsers.py
r44 r45 11 11 from collections import defaultdict 12 12 from collections import namedtuple 13 from itertools import izip 13 14 14 15 SEPARATOR = '--gc0p4Jq0M2Yt08jU534c0p' … … 46 47 """ 47 48 def __init__(self, 49 protein_factory, 50 peptide_factory, 51 spectrum_factory, 52 psm_factory, 48 53 scan_str=r'FinneganScanNumber%3a%20(\d+)%20', 49 54 rawfn_str=r'RawFile%3a%20(.+raw)', … … 51 56 contaminant_str=r'^IPI:CON_:IPI', 52 57 # XXX: Fix default factories 53 protein_factory=dict,54 peptide_factory=dict,55 spectrum_factory=dict,56 psm_factory=dict57 58 ): 58 59 self.scan_regex = re.compile(scan_str) … … 62 63 self.non_target_regexes = (contaminant_regex, decoy_regex) 63 64 self.rawfn_regex = re.compile(rawfn_str) 65 self.protein_factory = protein_factory 66 self.peptide_factory = protein_factory 67 self.spectrum_factory=spectrum_factory 68 self.psm_factory=psm_factory 64 69 65 70 def _parse_spectra_fn(self, dat_file): … … 168 173 nativeid_psms = self._parse_psms(dat_file) 169 174 extraspec = self._parse_extraspec(dat_file) 170 #for native_id, psms in nativeid_psms.items(): 171 # for psm in psms: 172 # psm['#SpectraFile'] = pkl_fn 173 # psm['FragMode'] = frag_mode 174 # psm.update(nativeid_spectra[native_id]) 175 # yield psm 176 #return proteins, peptides, spectra, psms 175 spectra = dict() 176 for summ, extra in izip(summspec, extraspec): 177 spectrum = self.spectrum_factory(prec_mz=summ[0], 178 prec_charge=summ[1], 179 run=extra[0], 180 scan=extra[1], 181 peaks="TBI") 182 spectra[(spectrum.scan, spectrum.run)] = spectrum 183 import ipdb; ipdb.set_trace() 184 return proteins, peptides, spectra, psms 177 185 178 186 def get_prot_ids(accs):
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