def assemble_locus(transcripts, locus_id_value_obj, gene_id_value_obj,
tss_id_value_obj, t_id_value_obj, config, gtf_fileh,
bed_fileh, bedgraph_filehs):
# gather properties of locus
locus_chrom = transcripts[0].chrom
locus_start = transcripts[0].start
locus_end = max(tx.end for tx in transcripts)
logging.debug("[LOCUS] %s:%d-%d %d transcripts" %
(locus_chrom, locus_start, locus_end, len(transcripts)))
locus_id_str = "L%d" % (locus_id_value_obj.next())
# filter transcripts
logging.debug("\tFiltering transcripts")
transcripts = filter_transcripts(transcripts, config.min_transcript_length,
config.guided)
# build transcript graphs
transcript_graphs = \
create_transcript_graphs(locus_chrom, transcripts,
min_trim_length=config.min_trim_length,
trim_utr_fraction=config.trim_utr_fraction,
trim_intron_fraction=config.trim_intron_fraction,
create_bedgraph=config.create_bedgraph,
bedgraph_filehs=bedgraph_filehs)
for tg in transcript_graphs:
logging.debug(
"Subgraph %s:%d-%d(%s) %d nodes %d paths" %
(locus_chrom, locus_start, locus_end, strand_int_to_str(
tg.strand), len(tg.Gsub), len(tg.partial_paths)))
# assemble subgraph
assemble_gene(locus_chrom, locus_id_str, gene_id_value_obj,
tss_id_value_obj, t_id_value_obj, tg.Gsub, tg.strand,
tg.partial_paths, config, gtf_fileh, bed_fileh)
def assemble_locus(
transcripts,
locus_id_value_obj,
gene_id_value_obj,
tss_id_value_obj,
t_id_value_obj,
config,
gtf_fileh,
bed_fileh,
bedgraph_filehs,
):
def get_bedgraph_lines(chrom, G):
for n in sorted(G.nodes()):
if n.start < 0:
continue
fields = (chrom, n.start, n.end, G.node[n][NODE_SCORE])
yield fields
# gather properties of locus
locus_chrom = transcripts[0].chrom
locus_start = transcripts[0].start
locus_end = max(tx.end for tx in transcripts)
logging.debug("[LOCUS] %s:%d-%d %d transcripts" % (locus_chrom, locus_start, locus_end, len(transcripts)))
locus_id_str = "L%d" % (locus_id_value_obj.next())
# filter transcripts
logging.debug("\tFiltering transcripts")
transcripts = filter_transcripts(transcripts, config.min_transcript_length, config.guided)
# build transcript graphs
for G, strand, strand_transcripts in create_transcript_graphs(transcripts):
# output bedgraph
if config.create_bedgraph:
for fields in get_bedgraph_lines(locus_chrom, G):
print >>bedgraph_filehs[strand], "\t".join(map(str, fields))
# process transcript graphs
for Gsub, strand, partial_paths in prune_transcript_graph(
G, strand, strand_transcripts, config.min_trim_length, config.trim_utr_fraction, config.trim_intron_fraction
):
logging.debug(
"Subgraph %s:%d-%d(%s) %d nodes %d paths"
% (locus_chrom, locus_start, locus_end, strand_int_to_str(strand), len(Gsub), len(partial_paths))
)
# assemble subgraph
assemble_gene(
locus_chrom,
locus_id_str,
gene_id_value_obj,
tss_id_value_obj,
t_id_value_obj,
Gsub,
strand,
partial_paths,
config,
gtf_fileh,
bed_fileh,
)
def assemble_locus(transcripts,
locus_id_value_obj,
gene_id_value_obj,
tss_id_value_obj,
t_id_value_obj,
config,
gtf_fileh,
bed_fileh,
bedgraph_filehs):
def get_bedgraph_lines(chrom, G):
for n in sorted(G.nodes()):
if n.start < 0:
continue
fields = (chrom, n.start, n.end, G.node[n][NODE_SCORE])
yield fields
# gather properties of locus
locus_chrom = transcripts[0].chrom
locus_start = transcripts[0].start
locus_end = max(tx.end for tx in transcripts)
logging.debug("[LOCUS] %s:%d-%d %d transcripts" %
(locus_chrom, locus_start, locus_end,
len(transcripts)))
locus_id_str = "L%d" % (locus_id_value_obj.next())
# filter transcripts
logging.debug("\tFiltering transcripts")
transcripts = filter_transcripts(transcripts,
config.min_transcript_length,
config.guided)
# build transcript graphs
for G, strand, strand_transcripts in \
create_transcript_graphs(transcripts):
# output bedgraph
if config.create_bedgraph:
for fields in get_bedgraph_lines(locus_chrom, G):
print >>bedgraph_filehs[strand], '\t'.join(map(str,fields))
# process transcript graphs
for Gsub, strand, partial_paths in \
prune_transcript_graph(G, strand, strand_transcripts,
config.min_trim_length,
config.trim_utr_fraction,
config.trim_intron_fraction):
logging.debug("Subgraph %s:%d-%d(%s) %d nodes %d paths" %
(locus_chrom, locus_start, locus_end,
strand_int_to_str(strand), len(Gsub),
len(partial_paths)))
# assemble subgraph
assemble_gene(locus_chrom, locus_id_str,
gene_id_value_obj,
tss_id_value_obj,
t_id_value_obj,
Gsub, strand, partial_paths,
config,
gtf_fileh,
bed_fileh)
def assemble_locus(transcripts,
locus_id_value_obj,
gene_id_value_obj,
tss_id_value_obj,
t_id_value_obj,
config,
gtf_fileh,
bed_fileh,
bedgraph_filehs):
# gather properties of locus
locus_chrom = transcripts[0].chrom
locus_start = transcripts[0].start
locus_end = max(tx.end for tx in transcripts)
logging.debug("[LOCUS] %s:%d-%d %d transcripts" %
(locus_chrom, locus_start, locus_end,
len(transcripts)))
locus_id_str = "L%d" % (locus_id_value_obj.next())
# filter transcripts
logging.debug("\tFiltering transcripts")
transcripts = filter_transcripts(transcripts,
config.min_transcript_length,
config.guided)
# build transcript graphs
transcript_graphs = \
create_transcript_graphs(locus_chrom, transcripts,
min_trim_length=config.min_trim_length,
trim_utr_fraction=config.trim_utr_fraction,
trim_intron_fraction=config.trim_intron_fraction,
create_bedgraph=config.create_bedgraph,
bedgraph_filehs=bedgraph_filehs)
for tg in transcript_graphs:
logging.debug("Subgraph %s:%d-%d(%s) %d nodes %d paths" %
(locus_chrom, locus_start, locus_end,
strand_int_to_str(tg.strand), len(tg.Gsub),
len(tg.partial_paths)))
# assemble subgraph
assemble_gene(locus_chrom, locus_id_str,
gene_id_value_obj,
tss_id_value_obj,
t_id_value_obj,
tg.Gsub, tg.strand, tg.partial_paths,
config,
gtf_fileh,
bed_fileh)
def get_transcript_graphs(transcripts):
GG = {}
for G, strand, strand_transcript_map in \
create_transcript_graphs(transcripts):
GG[strand] = (G, strand_transcript_map)
return GG
def get_transcript_graphs(transcripts):
GG = {}
for G, strand, strand_transcript_map in \
create_transcript_graphs(transcripts):
GG[strand] = (G, strand_transcript_map)
return GG