def main(argv=sys.argv[1:]):
"""Command-line program
Parameters
----------
argv : list, optional
A list of command-line arguments, which will be processed
as if the script were called from the command line if
:py:func:`main` is called directly.
Default: sys.argv[1:] (actually command-line arguments)
"""
ap = AnnotationParser(input_choices=_ANNOTATION_INPUT_CHOICES)
annotation_file_parser = ap.get_parser()
bp = BaseParser()
base_parser = bp.get_parser()
parser = argparse.ArgumentParser(description=format_module_docstring(__doc__),
formatter_class=argparse.RawDescriptionHelpFormatter,
parents=[base_parser,annotation_file_parser])
parser.add_argument("--export_tophat",default=False,action="store_true",
help="Export tophat `.juncs` file in addition to BED output")
parser.add_argument("outbase",type=str,help="Basename for output files")
args = parser.parse_args(argv)
bp.get_base_ops_from_args(args)
transcripts = ap.get_transcripts_from_args(args,printer=printer,return_type=SegmentChain)
with argsopener("%s.bed" % args.outbase,args,"w") as bed_out:
if args.export_tophat == True:
tophat_out = open("%s.juncs" % args.outbase,"w")
printer.write("params: " +" ".join(argv))
printer.write("Detecting & comparing junctions...")
ex_pairs = {}
c = 0
u = 0
for chain in transcripts:
if len(chain) > 1: # if multi-exon
chrom = chain.chrom
strand = chain.strand
try:
ep = ex_pairs[(chrom,strand)]
except KeyError:
ex_pairs[(chrom,strand)] = []
ep = ex_pairs[(chrom,strand)]
for i in range(0,len(chain)-1):
seg1 = chain[i]
seg2 = chain[i+1]
if c % 1000 == 0 and c > 0:
printer.write("Processed %s junctions. Found %s unique..." % (c,u) )
c+=1
key = (seg1.end,seg2.start)
if key not in ep:
ep.append(key)
u += 1
new_chain = SegmentChain(seg1,seg2)
bed_out.write(new_chain.as_bed())
if args.export_tophat == True:
my_junc = (chrom,seg1.end-1,seg2.start,strand)
tophat_out.write("%s\t%s\t%s\t%s\n" % my_junc)
del new_chain
del seg1
del seg2
del chain
printer.write("Processed %s total junctions. Found %s unique." % (c,u) )
bed_out.close()
if args.export_tophat == True:
tophat_out.close()
printer.write("Done.")
def process_partial_group(transcripts, mask_hash, printer):
"""Correct boundaries of merged genes, as described in :func:`do_generate`
Parameters
----------
transcripts : dict
Dictionary mapping unique transcript IDs to |Transcripts|.
This set should be complete in the sense that it should contain
all transcripts that have any chance of mutually overlapping
each other (e.g. all on same chromosome and strand).
mask_hash : |GenomeHash|
|GenomeHash| of regions to exclude from analysis
Returns
-------
:class:`pandas.DataFrame`
Table of merged gene positions
:class:`pandas.DataFrame`
Table of adjusted transcript positions
:class:`dict`
Dictionary mapping raw gene names to merged gene names
"""
gene_table = {
"region": [],
"transcript_ids": [],
"exon_unmasked": [],
"exon": [],
"masked": [],
"utr5": [],
"cds": [],
"utr3": [],
"exon_bed": [],
"utr5_bed": [],
"cds_bed": [],
"utr3_bed": [],
"masked_bed": [],
}
# data table for transcripts
transcript_table = {
"region": [],
"exon": [],
"utr5": [],
"cds": [],
"utr3": [],
"masked": [],
"exon_unmasked": [],
"transcript_ids": [],
"exon_bed": [],
"utr5_bed": [],
"cds_bed": [],
"utr3_bed": [],
"masked_bed": [],
}
keycombos = list(itertools.permutations(("utr5", "cds", "utr3"), 2))
# merge genes that share exons & write output
printer.write("Collapsing genes that share exons ...")
merged_genes = merge_genes(transcripts)
# remap transcripts to merged genes
# and vice-versa
merged_gene_tx = {}
tx_merged_gene = {}
printer.write("Mapping transcripts to merged genes...")
for txid in transcripts:
my_tx = transcripts[txid]
my_gene = my_tx.get_gene()
my_merged = merged_genes[my_gene]
tx_merged_gene[txid] = my_merged
try:
merged_gene_tx[my_merged].append(txid)
except KeyError:
merged_gene_tx[my_merged] = [txid]
# flatten merged genes
printer.write(
"Flattening merged genes, masking positions, and labeling subfeatures ..."
)
for n, (gene_id, my_txids) in enumerate(merged_gene_tx.items()):
if n % 1000 == 0 and n > 0:
printer.write(" %s genes ..." % n)
my_gene_positions = []
chroms = []
strands = []
for my_txid in my_txids:
my_segmentchain = transcripts[my_txid]
chroms.append(my_segmentchain.chrom)
strands.append(my_segmentchain.strand)
my_gene_positions.extend(my_segmentchain.get_position_list())
try:
assert len(set(chroms)) == 1
except AssertionError:
printer.write(
"Skipping gene %s which contains multiple chromosomes: %s"
% (gene_id, ",".join(chroms)))
try:
assert len(set(strands)) == 1
except AssertionError:
printer.write(
"Skipping gene %s which contains multiple strands: %s" %
(gene_id, ",".join(strands)))
my_gene_positions = set(my_gene_positions)
gene_ivc_raw = SegmentChain(
*positions_to_segments(chroms[0], strands[0], my_gene_positions))
gene_table["region"].append(gene_id)
gene_table["transcript_ids"].append(",".join(sorted(my_txids)))
gene_table["exon_unmasked"].append(gene_ivc_raw)
printer.write(" %s genes total." % (n + 1))
# mask genes
printer.write("Masking positions and labeling subfeature positions ...")
gene_hash = GenomeHash(gene_table["exon_unmasked"], do_copy=False)
for n, (gene_id, gene_ivc_raw) in enumerate(
zip(gene_table["region"], gene_table["exon_unmasked"])):
if n % 2000 == 0:
printer.write(" %s genes ..." % n)
my_chrom = gene_ivc_raw.spanning_segment.chrom
my_strand = gene_ivc_raw.spanning_segment.strand
masked_positions = []
nearby_genes = gene_hash[gene_ivc_raw]
# don't mask out positions from identical gene
gene_ivc_raw_positions = gene_ivc_raw.get_position_set()
nearby_genes = [
X for X in nearby_genes
if X.get_position_set() != gene_ivc_raw_positions
]
for gene in nearby_genes:
masked_positions.extend(gene.get_position_list())
nearby_masks = mask_hash[gene_ivc_raw]
for mask in nearby_masks:
masked_positions.extend(mask.get_position_list())
masked_positions = set(masked_positions)
gene_positions_raw = gene_ivc_raw.get_position_set()
mask_ivc_positions = gene_positions_raw & masked_positions
total_mask_ivc = SegmentChain(*positions_to_segments(
my_chrom, my_strand, mask_ivc_positions),
ID=gene_id)
gene_table["masked"].append(total_mask_ivc)
gene_table["masked_bed"].append(total_mask_ivc.as_bed())
gene_post_mask = gene_positions_raw - masked_positions
gene_post_mask_ivc = SegmentChain(*positions_to_segments(
my_chrom, my_strand, gene_post_mask),
ID=gene_id)
gene_table["exon"].append(gene_post_mask_ivc)
gene_table["exon_bed"].append(gene_post_mask_ivc.as_bed())
masked_positions = total_mask_ivc.get_position_set()
tmp_positions = {
"utr5": set(),
"cds": set(),
"utr3": set(),
}
txids = sorted(merged_gene_tx[gene_id])
chrom = gene_post_mask_ivc.chrom
strand = gene_post_mask_ivc.strand
# pool transcript positions
for txid in txids:
transcript = transcripts[txid]
utr5pos = transcript.get_utr5().get_position_set()
cdspos = transcript.get_cds().get_position_set()
utr3pos = transcript.get_utr3().get_position_set()
tmp_positions["utr5"] |= utr5pos
tmp_positions["cds"] |= cdspos
tmp_positions["utr3"] |= utr3pos
# eliminate positions in which CDS & UTRs overlap from each transcript
for txid in txids:
transcript = transcripts[txid]
transcript_positions = {
"utr5": transcript.get_utr5().get_position_set(),
"cds": transcript.get_cds().get_position_set(),
"utr3": transcript.get_utr3().get_position_set(),
}
for key1, key2 in keycombos:
transcript_positions[key1] -= tmp_positions[key2]
transcript_positions[key1] -= masked_positions
transcript_table["region"].append(txid)
# all unmasked positions
my_chain = SegmentChain(*positions_to_segments(
chrom, strand,
transcript.get_position_set() - masked_positions),
ID=txid)
transcript_table["exon"].append(str(my_chain))
transcript_table["exon_bed"].append(my_chain.as_bed())
# all uniquely-labeled unmasked positions
for k, v in transcript_positions.items():
my_chain = SegmentChain(*positions_to_segments(
chrom, strand, v),
ID=txid)
transcript_table[k].append(str(my_chain))
transcript_table["%s_bed" % k].append(my_chain.as_bed())
total_mask_ivc.attr["ID"] = txid
transcript_table["masked"].append(str(total_mask_ivc))
transcript_table["masked_bed"].append(total_mask_ivc.as_bed())
transcript_table["exon_unmasked"].append(str(transcript))
transcript_table["transcript_ids"].append(txid)
tmp_positions2 = copy.deepcopy(tmp_positions)
for k1, k2 in keycombos:
tmp_positions[k1] -= tmp_positions2[k2]
tmp_positions[k1] -= masked_positions
for k in (tmp_positions.keys()):
my_chain = SegmentChain(*positions_to_segments(
chrom, strand, tmp_positions[k]),
ID=gene_id)
gene_table[k].append(str(my_chain))
gene_table["%s_bed" % k].append(my_chain.as_bed())
printer.write(" %s genes total." % (n + 1))
# cast SegmentChains/Transcripts to strings to keep numpy from unpacking them
conversion_keys = [
"exon", "utr5", "cds", "utr3", "masked", "exon_unmasked"
]
for k in conversion_keys:
gene_table[k] = [str(X) for X in gene_table[k]]
transcript_table[k] = [str(X) for X in transcript_table[k]]
gene_df = pd.DataFrame(gene_table)
gene_df.sort_values(["region"], inplace=True)
transcript_df = pd.DataFrame(transcript_table)
transcript_df.sort_values(["region"], inplace=True)
return gene_df, transcript_df, merged_genes