feature_coords = load(open(feature_coords_fn))
print >> stderr, "Note: using FASTA file at %s" % fastafn
f = open(gtffn)
junctions = set()
for row in f: # for each row in the input GTF
# we need to get rid of first and last exons
if row.strip().split('\t')[2] in ['start_codon', 'stop_codon', 'CDS']:
continue
if feature_coords_fn: # if we have the resource to check whether this is a terminal exon or not
# print >> stderr,row.strip()
strand = row.strip().split('\t')[6]
feature, blank = parse_lines([row.strip()], strand, get_transcripts)
# print >> stderr,feature
is_terminal_feature, up_exon, down_exon = terminal_exon(
list(feature)[0], feature_coords)
if is_terminal_feature: # if this is terminal ignore it
continue
# now we know that this is not a terminal exon so there must be neighbouring exons
up_exon_gtf = region_to_GTF(up_exon, feature_coords[up_exon],
get_transcripts)
down_exon_gtf = region_to_GTF(down_exon, feature_coords[down_exon],
get_transcripts)
if get_introns:
up_exon_five, up_exon_three = GTFrow_to_5p3pcoords(
up_exon_gtf, offset, use_chromnames)
five, three = GTFrow_to_5p3pcoords(row, offset, use_chromnames)
down_exon_five, down_exon_three = GTFrow_to_5p3pcoords(
down_exon_gtf, offset, use_chromnames)
junctions.add((up_exon_five, three, five, down_exon_three))
o = open(ofn, 'w')
o_before = open(ofn + ".before", 'w')
o_after = open(ofn + ".after", 'w')
print >> stderr, "Extending exonic regions by %s bases. Specify your own with option '-e' (see help for details)" % extend
exons = list()
for row in open(exonfn):
h1 = row.strip().split('\t')[1]
for h in h1.split(','):
exons.append(h)
gex_coords = load(open(gexons_pic))
tabixfile = pysam.Tabixfile(tabixfn)
for exon in exons:
is_terminal_exon, prev_exon, next_exon = terminal_exon(exon, gex_coords)
if is_terminal_exon: continue
# get the coordinates
coords = augment_region(gex_coords[exon], extend)
coords_before = augment_region(gex_coords[prev_exon], extend)
coords_after = augment_region(gex_coords[next_exon], extend)
# whether to use 'chr' or not
if not use_chrom_names:
coords = coords[3:]
coords_before = coords_before[3:]
coords_after = coords_after[3:]
# get the GTF rows that satisfy this
rows = [
o = open(ofn,'w')
o_before = open(ofn+".before",'w')
o_after = open(ofn+".after",'w')
print >> stderr,"Extending exonic regions by %s bases. Specify your own with option '-e' (see help for details)"%extend
exons = list()
for row in open(exonfn):
h1 = row.strip().split('\t')[1]
for h in h1.split(','):
exons.append(h)
gex_coords = load(open(gexons_pic))
tabixfile = pysam.Tabixfile(tabixfn)
for exon in exons:
is_terminal_exon,prev_exon,next_exon = terminal_exon(exon,gex_coords)
if is_terminal_exon: continue
# get the coordinates
coords = augment_region(gex_coords[exon],extend)
coords_before = augment_region(gex_coords[prev_exon],extend)
coords_after = augment_region(gex_coords[next_exon],extend)
# whether to use 'chr' or not
if not use_chrom_names:
coords = coords[3:]
coords_before = coords_before[3:]
coords_after = coords_after[3:]
# get the GTF rows that satisfy this
rows = [row for row in tabixfile.fetch(region=coords) if row.strip().split('\t')[2] == "exon"]
if feature_coords_fn:
feature_coords = load(open(feature_coords_fn))
print >> stderr,"Note: using FASTA file at %s" % fastafn
f = open(gtffn)
junctions = set()
for row in f: # for each row in the input GTF
# we need to get rid of first and last exons
if row.strip().split('\t')[2] in ['start_codon','stop_codon','CDS']: continue
if feature_coords_fn: # if we have the resource to check whether this is a terminal exon or not
# print >> stderr,row.strip()
strand = row.strip().split('\t')[6]
feature,blank = parse_lines([row.strip()],strand,get_transcripts)
# print >> stderr,feature
is_terminal_feature,up_exon,down_exon = terminal_exon(list(feature)[0],feature_coords)
if is_terminal_feature: # if this is terminal ignore it
continue
# now we know that this is not a terminal exon so there must be neighbouring exons
up_exon_gtf = region_to_GTF(up_exon,feature_coords[up_exon],get_transcripts)
down_exon_gtf = region_to_GTF(down_exon,feature_coords[down_exon],get_transcripts)
if get_introns:
up_exon_five,up_exon_three = GTFrow_to_5p3pcoords(up_exon_gtf,offset,use_chromnames)
five,three = GTFrow_to_5p3pcoords(row,offset,use_chromnames)
down_exon_five,down_exon_three = GTFrow_to_5p3pcoords(down_exon_gtf,offset,use_chromnames)
junctions.add((up_exon_five,three,five,down_exon_three))
else:
five,three = GTFrow_to_5p3pcoords(row,offset,use_chromnames)
junctions.add((five,three))
f.close()
