def __init__(self,genome_2bit_file,verbose=False): self.genome=TwoBitFile(open(genome_2bit_file,'rb')) self.chr_len=dict() self.verbose=verbose for chr_id in self.genome.keys(): self.chr_len[chr_id]=len(self.genome[chr_id]) if verbose: print 'Genome initializated'
def _get_reference_data(twobit_file_name, chrom, low, high): # Read and return reference data. try: with open(twobit_file_name, 'rb') as f: twobit = TwoBitFile(f) if chrom in twobit: seq_data = twobit[chrom].get(int(low), int(high)) return GenomeRegion(chrom=chrom, start=low, end=high, sequence=seq_data) except OSError as e: raise e()
def reference(self, trans, dbkey, chrom, low, high): """ Return reference data for a build. """ self.check_and_reload() # If there is no dbkey owner, default to current user. dbkey_owner, dbkey = decode_dbkey(dbkey) if dbkey_owner: dbkey_user = trans.sa_session.query( trans.app.model.User).filter_by(username=dbkey_owner).first() else: dbkey_user = trans.user if not self.has_reference_data(dbkey, dbkey_user): return None # # Get twobit file with reference data. # twobit_file_name = None if dbkey in self.genomes: # Built-in twobit. twobit_file_name = self.genomes[dbkey].twobit_file else: user_keys = loads(dbkey_user.preferences['dbkeys']) dbkey_attributes = user_keys[dbkey] fasta_dataset = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation).get( dbkey_attributes['fasta']) msg = fasta_dataset.convert_dataset(trans, 'twobit') if msg: return msg else: twobit_dataset = fasta_dataset.get_converted_dataset( trans, 'twobit') twobit_file_name = twobit_dataset.file_name # Read and return reference data. try: twobit = TwoBitFile(open(twobit_file_name)) if chrom in twobit: seq_data = twobit[chrom].get(int(low), int(high)) return GenomeRegion(chrom=chrom, start=low, end=high, sequence=seq_data) except IOError: return None