def make_chimera(cluster_pair, cluster_shelve, transcript_dict,
genome_tx_trees, annotation_source):
# lookup 5' and 3' clusters
cluster5p = cluster_shelve[str(cluster_pair.id5p)]
cluster3p = cluster_shelve[str(cluster_pair.id3p)]
# get 5' and 3' transcripts
transcripts5p = lookup_transcripts(cluster5p, transcript_dict,
genome_tx_trees)
transcripts3p = lookup_transcripts(cluster3p, transcript_dict,
genome_tx_trees)
# lookup chimera type and distance
chimera_type, distance = get_chimera_type(cluster5p, cluster3p,
transcripts5p, transcripts3p,
transcript_dict, genome_tx_trees)
# format transcript information
tx_names_5p, gene_names_5p, biotypes_5p = get_transcript_info(
transcripts5p, annotation_source)
tx_names_3p, gene_names_3p, biotypes_3p = get_transcript_info(
transcripts3p, annotation_source)
# make chimera object
c = Chimera()
c.rname5p = cluster5p.rname
c.start5p = cluster5p.start
c.end5p = cluster5p.end
c.rname3p = cluster3p.rname
c.start3p = cluster3p.start
c.end3p = cluster3p.end
c.chimera_id = "CHIMERA%d" % (cluster_pair.pair_id)
frags = set(cluster_pair.qnames)
frags.update(cluster_pair.spanning_qnames)
c.num_frags = len(frags)
c.strand5p = cluster5p.strand
c.strand3p = cluster3p.strand
c.chimera_type = chimera_type
c.distance = distance
c.num_discordant_frags = len(cluster_pair.qnames)
c.num_spanning_frags = len(cluster_pair.spanning_qnames)
c.num_discordant_frags_5p = len(cluster5p.qnames)
c.num_discordant_frags_3p = len(cluster3p.qnames)
c.num_concordant_frags_5p = cluster5p.concordant_frags
c.num_concordant_frags_3p = cluster3p.concordant_frags
c.biotypes_5p = sorted(biotypes_5p)
c.biotypes_3p = sorted(biotypes_3p)
c.genes_5p = sorted(gene_names_5p)
c.genes_3p = sorted(gene_names_3p)
c.transcripts_5p = sorted(tx_names_5p)
c.transcripts_3p = sorted(tx_names_3p)
return c
def make_chimera(cluster_pair,
cluster_shelve,
transcript_dict,
genome_tx_trees,
annotation_source):
# lookup 5' and 3' clusters
cluster5p = cluster_shelve[str(cluster_pair.id5p)]
cluster3p = cluster_shelve[str(cluster_pair.id3p)]
# get 5' and 3' transcripts
transcripts5p = lookup_transcripts(cluster5p, transcript_dict, genome_tx_trees)
transcripts3p = lookup_transcripts(cluster3p, transcript_dict, genome_tx_trees)
# lookup chimera type and distance
chimera_type, distance = get_chimera_type(cluster5p, cluster3p,
transcripts5p, transcripts3p,
transcript_dict, genome_tx_trees)
# format transcript information
tx_names_5p, gene_names_5p, biotypes_5p = get_transcript_info(transcripts5p, annotation_source)
tx_names_3p, gene_names_3p, biotypes_3p = get_transcript_info(transcripts3p, annotation_source)
# make chimera object
c = Chimera()
c.rname5p = cluster5p.rname
c.start5p = cluster5p.start
c.end5p = cluster5p.end
c.rname3p = cluster3p.rname
c.start3p = cluster3p.start
c.end3p = cluster3p.end
c.chimera_id = "CHIMERA%d" % (cluster_pair.pair_id)
frags = set(cluster_pair.qnames)
frags.update(cluster_pair.spanning_qnames)
c.num_frags = len(frags)
c.strand5p = cluster5p.strand
c.strand3p = cluster3p.strand
c.chimera_type = chimera_type
c.distance = distance
c.num_discordant_frags = len(cluster_pair.qnames)
c.num_spanning_frags = len(cluster_pair.spanning_qnames)
c.num_discordant_frags_5p = len(cluster5p.qnames)
c.num_discordant_frags_3p = len(cluster3p.qnames)
c.num_concordant_frags_5p = cluster5p.concordant_frags
c.num_concordant_frags_3p = cluster3p.concordant_frags
c.biotypes_5p = sorted(biotypes_5p)
c.biotypes_3p = sorted(biotypes_3p)
c.genes_5p = sorted(gene_names_5p)
c.genes_3p = sorted(gene_names_3p)
c.transcripts_5p = sorted(tx_names_5p)
c.transcripts_3p = sorted(tx_names_3p)
return c
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
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
