def read_pairs_to_chimera(chimera_name, tid5p, tid3p, readpairs, tid_tx_map, genome_tx_trees, trim_bp): # get gene information tx5p = tid_tx_map[tid5p] tx3p = tid_tx_map[tid3p] # categorize chimera type chimera_type, distance = get_chimera_type(tx5p, tx3p, genome_tx_trees) # create chimera object c = Chimera() iter5p = itertools.imap(operator.itemgetter(0), readpairs) iter3p = itertools.imap(operator.itemgetter(1), readpairs) c.partner5p = ChimeraPartner.from_discordant_reads(iter5p, tx5p, trim_bp) c.partner3p = ChimeraPartner.from_discordant_reads(iter3p, tx3p, trim_bp) c.name = chimera_name c.chimera_type = chimera_type c.distance = distance # raw reads c.encomp_read_pairs = readpairs return c