| [24] | 1 | """Models for mzcms. |
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| 2 | |
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| 3 | """ |
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| [13] | 4 | from persistent import Persistent |
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| 5 | from repoze.folder import Folder |
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| [1] | 6 | |
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| [24] | 7 | from parsers import parse_dats |
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| 8 | |
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| [13] | 9 | class Experiment(Folder): |
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| [1] | 10 | __parent__ = __name__ = None |
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| [23] | 11 | def __init__(self, proteins, peptides, spectra, psms): |
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| 12 | super(Experiment, self).__init__() |
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| 13 | self['proteins'] = Proteins(proteins) |
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| 14 | self['peptides'] = Peptides(peptides) |
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| 15 | self['spectra'] = Spectra(spectra) |
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| 16 | self['psms'] = Psms(psms) |
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| [1] | 17 | |
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| [13] | 18 | class Proteins(Folder): |
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| [23] | 19 | """Proteins folder factory""" |
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| 20 | def __init__(self, proteins): |
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| [21] | 21 | self.name = 'proteins' |
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| [13] | 22 | |
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| 23 | class Protein(Persistent): |
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| [14] | 24 | """A Protein""" |
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| 25 | def __init__(self, native_id, sequence, pep_refs): |
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| 26 | self.sequence = str(native_id) |
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| 27 | self.sequence = str(sequence) |
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| [18] | 28 | self.pep_refs = tuple(pep_refs) |
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| [13] | 29 | |
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| 30 | class Peptides(Folder): |
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| [23] | 31 | """Peptides folder factory""" |
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| [21] | 32 | def __init__(self): |
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| 33 | self.name = 'peptides' |
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| [13] | 34 | |
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| 35 | class Peptide(Persistent): |
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| [17] | 36 | """A peptide""" |
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| 37 | def __init__(self, sequence, mass): |
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| 38 | self.sequence = str(sequence) |
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| 39 | self.mass = float(mass) |
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| 40 | self.length = len(sequence) |
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| [13] | 41 | |
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| [18] | 42 | class Spectra(Folder): |
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| [23] | 43 | """Spectra folder factory""" |
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| [21] | 44 | def __init__(self): |
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| 45 | self.name = 'spectra' |
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| [13] | 46 | |
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| [21] | 47 | |
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| [18] | 48 | class Spectrum(Persistent): |
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| [19] | 49 | """A Spectrum""" |
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| 50 | def __init__(self, scan, run, peaks, prec_mz, prec_charge): |
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| 51 | self.scan = int(scan) |
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| 52 | self.run = str(scan) |
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| 53 | self.peaks = tuple(peaks) |
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| 54 | self.prec_mz = float(prec_mz) |
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| 55 | self.prec_charge = int(prec_charge) |
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| [13] | 56 | |
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| [18] | 57 | class Psms(Folder): |
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| [23] | 58 | """Psms folder factory""" |
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| [21] | 59 | def __init__(self): |
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| 60 | self.name = 'psms' |
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| [13] | 61 | |
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| [18] | 62 | class Psm(Persistent): |
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| 63 | """A Peptide to Spectrum Match""" |
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| 64 | def __init__(self, score, rank, delta_mass, delta_score, |
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| 65 | sequence_rank2, pep_ref, spec_ref): |
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| 66 | self.score = float(score) |
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| 67 | self.rank = int(rank) |
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| 68 | self.delta_mass = float(delta_mass) |
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| 69 | self.delta_score = float(delta_score) |
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| 70 | self.sequence_rank2 = str(sequence_rank2) |
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| 71 | self.pep_ref = str(pep_ref) |
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| 72 | self.spec_ref = str(spec_ref) |
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| [13] | 73 | |
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| [1] | 74 | def appmaker(zodb_root): |
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| 75 | if not 'app_root' in zodb_root: |
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| [24] | 76 | data = parse_dats('./dats') |
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| 77 | app_root = Experiment(data) |
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| [23] | 78 | zodb_root['app_root'] = app_root |
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| [22] | 79 | import transaction |
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| 80 | transaction.commit() |
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| [21] | 81 | |
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| [1] | 82 | return zodb_root['app_root'] |
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