3aee104cf4c1e245dd020f743fbc58c17fd75976 mmaddren Mon Apr 9 12:12:44 2012 -0700 added encode.py to store global constants and other encode stuff, and made all other libraries interface correctly with it diff --git python/lib/ucscgenomics/mdb.py python/lib/ucscgenomics/mdb.py index c93e3b0..5c53cc5 100644 --- python/lib/ucscgenomics/mdb.py +++ python/lib/ucscgenomics/mdb.py @@ -1,257 +1,182 @@ -from ucscgenomics import ra, ordereddict - -class DataType(object): - - def __init__(self, name, molecule, strategy, source, selection, type): - self.name = name - self.molecule = molecule - self.strategy = strategy - self.source = source - self.selection = selection - self.type = type - - @property - def valid(self): - return self.molecule != 'REPLACE' and self.strategy != 'REPLACE' and self.source != 'REPLACE' and self.selection != 'REPLACE' and self.type != None - - @property - def shouldSubmit(self): - return self.type != 'NotGeo' - -dataTypes = { - 'Cage': DataType( 'Cage', 'RNA', 'OTHER', 'transcriptomic', 'CAGE', 'HighThroughput'), - 'ChipSeq': DataType( 'ChipSeq', 'genomic DNA', 'ChIP-Seq', 'genomic', 'ChIP', 'HighThroughput'), - 'DnaPet': DataType( 'DnaPet', 'genomic DNA', 'OTHER', 'genomic', 'size fractionation', 'HighThroughput'), - 'DnaseDgf': DataType( 'DnaseDgf', 'genomic DNA', 'DNase-Hypersensitivity', 'genomic', 'DNase', 'HighThroughput'), - 'DnaseSeq': DataType( 'DnaseSeq', 'genomic DNA', 'DNase-Hypersensitivity', 'genomic', 'DNase', 'HighThroughput'), - 'FaireSeq': DataType( 'FaireSeq', 'genomic DNA', 'OTHER', 'genomic', 'other', 'HighThroughput'), - 'MethylSeq': DataType( 'MethylSeq', 'genomic DNA', 'MRE-Seq', 'genomic', 'Restriction Digest', 'HighThroughput'), - 'MethylRrbs': DataType( 'MethylRrbs', 'genomic DNA', 'Bisulfite-Seq', 'genomic', 'Reduced Representation', 'HighThroughput'), - 'Orchid': DataType( 'Orchid', 'genomic DNA', 'OTHER', 'genomic', 'other', 'HighThroughput'), - 'Proteogenomics': DataType( 'Proteogenomics', 'protein', 'mass spectrometry-based proteogenomic mapping', 'protein', 'chromatographically fractionated peptides', 'HighThroughput'), - 'RnaPet': DataType( 'RnaPet', 'RNA', 'OTHER', 'transcriptomic', 'other', 'HighThroughput'), - 'RnaSeq': DataType( 'RnaSeq', 'RNA', 'RNA-Seq', 'transcriptomic', 'cDNA', 'HighThroughput'), - - #doublecheck - 'ChiaPet': DataType( 'ChiaPet', 'genomic DNA', 'ChIP-Seq followed by ligation', 'genomic', 'other', 'HighThroughput'), - 'Nucleosome': DataType( 'Nucleosome', 'genomic DNA', 'ChIP-Seq', 'genomic', 'ChIP', 'HighThroughput'), - 'RipSeq': DataType( 'RipSeq', 'RNA', 'OTHER', 'transcriptomic', 'RNA binding protein antibody', 'HighThroughput'), - #for ripseq, ask geo about new 'ripseq' - - #not geo stuff - '5C': DataType('5C', 'REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', 'NotGeo'), - 'Bip': DataType('Bip', 'REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', 'NotGeo'), - 'Gencode': DataType('Gencode', 'REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', 'NotGeo'), - 'Mapability': DataType('Mapability', 'REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', 'NotGeo'), - 'NRE': DataType('NRE', 'REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', 'NotGeo'), - 'Switchgear': DataType('Switchgear', 'REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', 'NotGeo'), - 'TfbsValid': DataType('TfbsValid', 'REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', 'NotGeo'), - 'Cluster': DataType('Cluster', 'REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', 'NotGeo'), - - #array - 'AffyExonArray': DataType( 'AffyExonArray', 'mRNA', 'RNA-Microarray', 'transcriptomic', 'polyA', 'MicroArray'), - 'MethylArray': DataType( 'MethylArray', 'genomic DNA', 'REPLACE', 'genomic', 'REPLACE', 'MicroArray'), - 'RipGeneSt': DataType( 'RipGeneSt', 'RNA', 'REPLACE', 'transcriptomic', 'RNA binding protein antibody', 'MicroArray'), #this isn't correct - 'RipTiling': DataType( 'RipTiling', 'RNA', 'REPLACE', 'transcriptomic', 'RNA binding protein antibody', 'MicroArray'), - - #these need to be curated - 'Cnv': DataType( 'Cnv', 'REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None), - 'Combined': DataType( 'Combined', 'REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None), - 'Genotype': DataType( 'Genotype', 'genomic DNA', 'REPLACE', 'genomic', 'REPLACE', None), - 'RnaChip': DataType( 'RnaChip', 'RNA', 'REPLACE', 'transcriptomic', 'RNA binding protein antibody', None), - 'RipChip': DataType( 'RipChip', 'RNA', 'REPLACE', 'transcriptomic', 'RNA binding protein antibody', None) - - -} - -#compare this to the source in datatype, give GP ids depending on the type -gpIds = { - 'human genomic': '63443', - 'human transcriptomic': '30709', - 'human protein': '63447', - - 'mouse genomic': '63471', - 'mouse transcriptomic': '66167', - 'mouse protein': '63475' -} +from ucscgenomics import ra, ordereddict, encode class MdbFile(ra.RaFile): ''' This should be used for all files in the metaDb, since they extend RaFile with useful functionality specific to metaDb ra files. ''' @property def name(self): return self.compositeStanza['metaObject'] @property def expVars(self): '''the experimental variables used in this track''' try: return self._expVars except AttributeError: self._expVars = self.compositeStanza['expVars'].split(',') return self._expVars @property def dataType(self): '''The data type of the experiment. 'None' if inconsistent.''' try: return self._dataType except AttributeError: self._dataType = None for e in self.experiments.itervalues(): if self._dataType == None and e.dataType != None: self._dataType = e.dataType elif self._dataType != e.dataType or e.dataType == None: self._dataType = None break return self._dataType @property def compositeStanza(self): '''the stanza (typically first in file) describing the composite''' try: return self._compositeStanza except AttributeError: self._compositeStanza = self.filter(lambda s: s['objType'] == 'composite', lambda s: s) if len(self._compositeStanza) != 1: raise KeyError(self.filename) else: self._compositeStanza = self._compositeStanza[0] return self._compositeStanza @property def experiments(self): '''dictionary of MdbExp objects indexed by the expId''' try: return self._experiments except AttributeError: self._experiments = dict() exps = self.filter(lambda s: s['objType'] != 'composite', lambda s: (s['expId'], s)) stanzas = dict() for k, v in exps: if k not in stanzas: stanzas[k] = list() stanzas[k].append(v) for id in stanzas.iterkeys(): self._experiments[id] = MdbExp(id, self, stanzas[id]) return self._experiments def __init__(self, filepath): ra.RaFile.__init__(self) self.read(filepath) def readStanza(self, stanza, key=None): entry = MdbStanza(self) if entry.readStanza(stanza, key) == None: return None, None, None val1, val2 = entry.readStanza(stanza, key) return val1, val2, entry def expIdRange(self, expIds): ''' Takes in a list of strings, and returns a list containing the valid range of expId keys that the inputted range encompasses. ''' ids = dict() tempids = list() for id in expIds: if '-' in id: start, end = id.split('-', 1) tempids.extend(range(int(start), int(end) + 1)) else: tempids.append(int(id)) for id in tempids: if str(id) in self.experiments.keys(): ids.append(str(id)) return ids class MdbStanza(ra.RaStanza): @property def title(self): '''The expVars catted together, making the title used for GEO''' try: return self._title except AttributeError: expVars = self._parent.expVars if expVars[0] in self: self._title = self[expVars[0]].replace('-m', '') else: self._title = None for expVar in expVars[1:len(expVars)]: if expVar in self and self[expVar] != 'None': self._title += '_' + self[expVar] return self._title def __init__(self, parent): ra.RaStanza.__init__(self) self._parent = parent def __setitem__(self, key, value): ordereddict.OrderedDict.__setitem__(self, key, value) ordereddict.OrderedDict.sort(self) ordereddict.OrderedDict.reorder(self, 0, 'metaObject') ordereddict.OrderedDict.reorder(self, 1, 'objType') class MdbExp(list): ''' Describes a single experiment ID, which has a collection of its stanzas as well as some additional data that should typically be consistent across all the stanzas, as well as verifying that the data is in fact consistent. ''' @property def name(self): return self._id @property def title(self): try: return self._title except AttributeError: self._title = None for s in self.normalStanzas: if self._title == None: self._title = s.title elif self._title != s.title: self._title = None break return self._title @property def dataType(self): '''The data type of the experiment. 'None' if inconsistent.''' try: return self._dataType except AttributeError: self._dataType = None for s in self.normalStanzas: if 'dataType' in s: if self._dataType == None: - self._dataType = dataTypes[s['dataType']] + self._dataType = encode.dataTypes[s['dataType']] elif self._dataType.name != s['dataType']: self._dataType = None break return self._dataType @property def normalStanzas(self): '''Returns the list of stanzas without revoked items''' try: return self._normal except AttributeError: self._normal = list() for s in self: if 'objStatus' not in s: self._normal.append(s) return self._normal def __init__(self, id, parent, stanzas): list.__init__(self) self.extend(stanzas) self._id = id self._parent = parent