Python Chimera.partner5p示例

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

示例#2

显示文件

文件： chimeras_to_breakpoints_v2.py 项目： BioXiao/chimerascan

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