def main():
usage = "usage: %prog [options] <gtf file>"
parser = OptionParser(usage)
parser.add_option(
"-c", dest="cds", action="store_true", default=False, help="Use CDS, not exons [Default: %default]"
)
(options, args) = parser.parse_args()
if len(args) != 1:
parser.error("Must provide gtf file")
else:
gtf_file = args[0]
genes = gff.read_genes(gtf_file)
for transcript_id in genes:
g = genes[transcript_id]
if options.cds:
block_sizes = ",".join([str(ex.end - ex.start + 1) for ex in g.cds])
block_starts = ",".join([str(ex.start - g.cds[0].start) for ex in g.cds])
cols = [
g.chrom,
str(g.cds[0].start - 1),
str(g.cds[-1].end),
transcript_id,
"0",
g.strand,
"0",
"0",
"255,0,0",
str(len(g.cds)),
block_sizes,
block_starts,
]
else:
block_sizes = ",".join([str(ex.end - ex.start + 1) for ex in g.exons])
block_starts = ",".join([str(ex.start - g.exons[0].start) for ex in g.exons])
cols = [
g.chrom,
str(g.exons[0].start - 1),
str(g.exons[-1].end),
transcript_id,
"0",
g.strand,
"0",
"0",
"255,0,0",
str(len(g.exons)),
block_sizes,
block_starts,
]
print "\t".join(cols)
def main():
usage = 'usage: %prog [options] <gtf file>'
parser = OptionParser(usage)
parser.add_option('-c',
dest='cds',
action='store_true',
default=False,
help='Use CDS, not exons [Default: %default]')
(options, args) = parser.parse_args()
if len(args) != 1:
parser.error('Must provide gtf file')
else:
gtf_file = args[0]
genes = gff.read_genes(gtf_file)
for transcript_id in genes:
g = genes[transcript_id]
if options.cds:
block_sizes = ','.join(
[str(ex.end - ex.start + 1) for ex in g.cds])
block_starts = ','.join(
[str(ex.start - g.cds[0].start) for ex in g.cds])
cols = [
g.chrom,
str(g.cds[0].start - 1),
str(g.cds[-1].end), transcript_id, '0', g.strand, '0', '0',
'255,0,0',
str(len(g.cds)), block_sizes, block_starts
]
else:
block_sizes = ','.join(
[str(ex.end - ex.start + 1) for ex in g.exons])
block_starts = ','.join(
[str(ex.start - g.exons[0].start) for ex in g.exons])
cols = [
g.chrom,
str(g.exons[0].start - 1),
str(g.exons[-1].end), transcript_id, '0', g.strand, '0', '0',
'255,0,0',
str(len(g.exons)), block_sizes, block_starts
]
print '\t'.join(cols)
def get_tss(gtf_file, upstream, downstream):
tss_intervals = {}
genes = gff.read_genes(gtf_file)
for gid in genes:
g = genes[gid]
if g.strand == '+':
istart = g.exons[0].start-upstream
iend = g.exons[0].start+downstream
else:
istart = g.exons[-1].end-downstream
iend = g.exons[-1].end+upstream
tss_intervals.setdefault(g.chrom,[]).append((istart,iend,g.strand,gid))
for chrom in tss_intervals:
tss_intervals[chrom].sort()
return tss_intervals
def get_tss(gtf_file, upstream, downstream):
tss_intervals = {}
genes = gff.read_genes(gtf_file)
for gid in genes:
g = genes[gid]
if g.strand == '+':
istart = g.exons[0].start - upstream
iend = g.exons[0].start + downstream
else:
istart = g.exons[-1].end - downstream
iend = g.exons[-1].end + upstream
tss_intervals.setdefault(g.chrom, []).append(
(istart, iend, g.strand, gid))
for chrom in tss_intervals:
tss_intervals[chrom].sort()
return tss_intervals
def main():
usage = 'usage: %prog [options] <ref_gtf>'
parser = OptionParser(usage)
#parser.add_option()
parser.add_option('-d', dest='downstream', type='int', default=1000, help='Downstream bp for promoters [Default: %default]')
parser.add_option('-f', dest='fpkm_tracking', help='Use cufflinks FPKM estimates to choose the most expressed isoform')
parser.add_option('-u', dest='upstream', type='int', default=1000, help='Upstream bp for promoters [Default: %default]')
(options,args) = parser.parse_args()
if len(args) != 1:
parser.error('Must provide reference GTF')
else:
ref_gtf = args[0]
g2t = gff.g2t(ref_gtf)
transcripts = gff.read_genes(ref_gtf)
source = open(ref_gtf).readline().split()[1]
if options.fpkm_tracking:
iso_fpkm_tracking = cufflinks.fpkm_tracking(options.fpkm_tracking)
for gene_id in g2t:
gene_transcripts = list(g2t[gene_id])
gene_strand = transcripts[gene_transcripts[0]].strand
if gene_strand not in ['+','-']:
print('WARNING: %s discluded for lack of strand' % gene_id, file=sys.stderr)
continue
# choose TSS
if options.fpkm_tracking:
# find most expressed isoform
promoter_tid = gene_transcripts[0]
max_fpkm = stats.geo_mean([1+fpkm for fpkm in iso_fpkm_tracking.gene_expr(promoter_tid)])
for transcript_id in gene_transcripts[1:]:
transcript_fpkm = stats.geo_mean([1+fpkm for fpkm in iso_fpkm_tracking.gene_expr(transcript_id)])
if math.isnan(max_fpkm) or transcript_fpkm > max_fpkm:
promoter_tid = transcript_id
max_fpkm = transcript_fpkm
# get isoform tss
if gene_strand == '+':
tss = transcripts[promoter_tid].exons[0].start
else:
tss = transcripts[promoter_tid].exons[-1].end
else:
# find most upstream tss
promoter_tid = gene_transcripts[0]
if gene_strand == '+':
upstream_tss = transcripts[promoter_tid].exons[0].start
else:
upstream_tss = transcripts[promoter_tid].exons[-1].end
for transcript_id in gene_transcripts[1:]:
if gene_strand == '+':
transcript_pos = transcripts[transcript_id].exons[0].start
if transcript_pos < upstream_tss:
promoter_tid = transcript_id
upstream_tss = transcript_pos
else:
transcript_pos = transcripts[transcript_id].exons[-1].end
if transcript_pos > upstream_tss:
promoter_tid = transcript_id
upstream_tss = transcript_pos
tss = upstream_tss
# print promoter from the tss
if gene_strand == '+':
if tss - options.upstream < 1:
print('WARNING: %s discluded for nearness to chromosome end' % gene_id, file=sys.stderr)
else:
tx = transcripts[promoter_tid]
cols = [tx.chrom, source, 'promoter', str(tss-options.upstream), str(tss+options.downstream), '.', tx.strand, '.', gff.kv_gtf(tx.kv)]
print('\t'.join(cols))
else:
if tss - options.downstream < 1:
print('WARNING: %s discluded for nearness to chromosome end' % gene_id, file=sys.stderr)
else:
tx = transcripts[promoter_tid]
cols = [tx.chrom, source, 'promoter', str(tss-options.downstream), str(tss+options.upstream), '.', tx.strand, '.', gff.kv_gtf(tx.kv)]
print('\t'.join(cols))
def get_splice_intervals(gtf_file, window):
intervals_5p = {}
intervals_3p = {}
genes = gff.read_genes(gtf_file)
for gid in genes:
g = genes[gid]
if len(g.exons) > 1:
if g.strand == '+':
# add first 5p site
exon = g.exons[0]
if not g.chrom in intervals_5p:
intervals_5p[g.chrom] = set()
intervals_5p[g.chrom].add((exon.end - window/2, exon.end + window/2, g.strand))
# process internal exons
for exon in g.exons[1:-1]:
# add 3p site
if not g.chrom in intervals_3p:
intervals_3p[g.chrom] = set()
intervals_3p[g.chrom].add((exon.start - window/2, exon.start + window/2, g.strand))
# add 5p site
if not g.chrom in intervals_5p:
intervals_5p[g.chrom] = set()
intervals_5p[g.chrom].add((exon.end - window/2, exon.end + window/2, g.strand))
# add last 3p site
exon = g.exons[-1]
if not g.chrom in intervals_3p:
intervals_3p[g.chrom] = set()
intervals_3p[g.chrom].add((exon.start - window/2, exon.start + window/2, g.strand))
else:
# add first 5p site
exon = g.exons[-1]
if not g.chrom in intervals_5p:
intervals_5p[g.chrom] = set()
intervals_5p[g.chrom].add((exon.end - window/2, exon.end + window/2, g.strand))
# process internal exons (in reverse order, but doesn't matter)
for exon in g.exons[1:-1]:
# add 3p site
if not g.chrom in intervals_3p:
intervals_3p[g.chrom] = set()
intervals_3p[g.chrom].add((exon.start - window/2, exon.start + window/2, g.strand))
# add 5p site
if not g.chrom in intervals_5p:
intervals_5p[g.chrom] = set()
intervals_5p[g.chrom].add((exon.end - window/2, exon.end + window/2, g.strand))
# add last 3p site
exon = g.exons[0]
if not g.chrom in intervals_3p:
intervals_3p[g.chrom] = set()
intervals_3p[g.chrom].add((exon.start - window/2, exon.start + window/2, g.strand))
# convert sets to sorted lists
for chrom in intervals_5p:
intervals_5p[chrom] = sorted(list(intervals_5p[chrom]))
intervals_3p[chrom] = sorted(list(intervals_3p[chrom]))
return intervals_5p, intervals_3p
def compute_coverage(anchor_gff, event_files, mode, anchor_is_gtf, bins):
############################################
# initialize
############################################
coverage = initialize_coverage(anchor_gff, mode, anchor_is_gtf, bins)
if anchor_is_gtf:
# get transcript structures
transcripts = gff.read_genes(anchor_gff, key_id='transcript_id')
# compute lengths
transcript_lengths = {}
for tid in transcripts:
tx = transcripts[tid]
for exon in tx.exons:
transcript_lengths[tid] = transcript_lengths.get(tid,0) + exon.end-exon.start+1
else:
transcripts = None
transcript_lengths = None
events = 0
for event_file in event_files:
print >> sys.stderr, 'Computing coverage for %s' % event_file
############################################
# preprocess BAM/GFF
############################################
if event_file[-4:] == '.bam':
# count fragments and hash multi-mappers
multi_maps = {}
for aligned_read in pysam.Samfile(event_file, 'rb'):
try:
nh_tag = aligned_read.opt('NH')
except:
nh_tag = 1.0
if aligned_read.is_paired:
events += 0.5/nh_tag
else:
events += 1.0/nh_tag
if nh_tag > 1:
multi_maps[aligned_read.qname] = nh_tag
elif event_file[-4:] == '.gff':
for line in open(event_file):
events += 1
else:
print >> sys.stderr, 'Unknown event file format %s' % event_file
############################################
# intersect BAM w/ anchors
############################################
if event_file[-4:] == '.bam':
p = subprocess.Popen('intersectBed -split -wo -bed -abam %s -b %s' % (event_file, anchor_gff), shell=True, stdout=subprocess.PIPE)
else:
p = subprocess.Popen('intersectBed -s -wo -a %s -b %s' % (event_file, anchor_gff), shell=True, stdout=subprocess.PIPE)
for line in p.stdout:
a = line.split('\t')
if event_file[-4:] == '.bam':
rstart = int(a[1])+1 # convert back to 1-based gff from bed
rend = int(a[2])
rheader = a[3]
else:
rstart = int(a[3])
rend = int(a[4])
# because intersectBed screws up indels near endpoints
if rstart < rend:
if event_file[-4:] == '.bam':
acol = 12
else:
acol = 9
achrom = a[acol]
astart = int(a[acol+3])
aend = int(a[acol+4])
astrand = a[acol+6]
if anchor_is_gtf:
anchor_id = gff.gtf_kv(a[acol+8])['transcript_id']
else:
anchor_id = (achrom, astart, aend)
# find where to increment
inc_start, inc_end = find_inc_coords(anchor_id, astart, aend, astrand, rstart, rend, mode, bins, transcripts, transcript_lengths)
if inc_start != None:
if event_file[-4:] == '.bam':
# find multi-map number, which may require removing a suffix
if rheader in multi_maps:
mm = multi_maps[rheader]
else:
rheader_base = rheader[:rheader.rfind('/')]
if rheader_base in multi_maps:
mm = multi_maps[rheader_base]
else:
mm = 1.0
else:
mm = 1.0
# increment!
for i in range(inc_start, inc_end):
coverage[anchor_id][i] += 1.0/mm
p.communicate()
return coverage, events
def main():
usage = 'usage: %prog [options] <ref_gtf> <prerna_gtf>'
parser = OptionParser(usage)
parser.add_option('-m', dest='max_genes_overlapped', default=None, type='int', help='Don\'t include isoforms that overlap more than this many genes [Default: %default]')
(options,args) = parser.parse_args()
if len(args) != 2:
parser.error('Must provide reference GTF and output prerna GTF')
else:
ref_gtf = args[0]
prerna_gtf = args[1]
# read transcripts for filtering/processing
transcripts = gff.read_genes(ref_gtf, key_id='transcript_id')
# add unspliced single exon transcripts to hash
prerna_hash = set()
for tid in transcripts:
tx = transcripts[tid]
if len(tx.exons) == 1:
tx_key = (tx.chrom, tx.exons[0].start, tx.exons[0].end, tx.strand)
prerna_hash.add(tx_key)
# process transcripts
prerna_out = open(prerna_gtf, 'w')
prerna_index = 0
for tid in transcripts:
tx = transcripts[tid]
pre_start = tx.exons[0].start
pre_end = tx.exons[-1].end
pre_key = (tx.chrom, pre_start, pre_end, tx.strand)
# print exons
for i in range(len(tx.exons)):
cols = (tx.chrom, 'dk', 'exon', str(tx.exons[i].start), str(tx.exons[i].end), '.', tx.strand, '.', gff.kv_gtf(tx.kv))
print >> prerna_out, '\t'.join(cols)
# print prernas
if not pre_key in prerna_hash:
prerna_hash.add(pre_key)
pre_kv = copy.copy(tx.kv)
pre_kv['transcript_id'] = 'PRERNA%d' % prerna_index
pre_kv['transcript_type'] = 'prerna'
prerna_index += 1
cols = (tx.chrom, 'dk', 'exon', str(pre_start), str(pre_end), '.', tx.strand, '.', gff.kv_gtf(pre_kv))
print >> prerna_out, '\t'.join(cols)
prerna_out.close()
if options.max_genes_overlapped != None:
# intersect with self and compute overlap sets
p = subprocess.Popen('intersectBed -wo -s -a %s -b %s' % (prerna_gtf, prerna_gtf), shell=True, stdout=subprocess.PIPE)
tx_overlaps = {}
for line in p.stdout:
a = line.split('\t')
kv1 = gff.gtf_kv(a[8])
tid1 = kv1['transcript_id']
if tid1.startswith('PRERNA'):
gid1 = kv1['gene_id']
gid2 = gff.gtf_kv(a[17])['gene_id']
if gid1 != gid2:
tx_overlaps.setdefault(tid1,set()).add(gid2)
p.communicate()
# filter into a temp gtf
prerna_tmp_fd, prerna_tmp_file = tempfile.mkstemp()
prerna_out = open(prerna_tmp_file, 'w')
for line in open(prerna_gtf):
a = line.split('\t')
kv = gff.gtf_kv(a[8])
tid = kv['transcript_id']
if len(tx_overlaps.get(tid,[])) <= options.max_genes_overlapped:
print >> prerna_out, line,
prerna_out.close()
# rewrite temp to the final output
prerna_out = open(prerna_gtf, 'w')
for line in open(prerna_tmp_file):
print >> prerna_out, line,
prerna_out.close()
os.close(prerna_tmp_fd)
os.remove(prerna_tmp_file)
def main():
usage = 'usage: %prog [options] <ref_gtf> <prerna_gtf>'
parser = OptionParser(usage)
parser.add_option(
'-m',
dest='max_genes_overlapped',
default=None,
type='int',
help=
'Don\'t include isoforms that overlap more than this many genes [Default: %default]'
)
(options, args) = parser.parse_args()
if len(args) != 2:
parser.error('Must provide reference GTF and output prerna GTF')
else:
ref_gtf = args[0]
prerna_gtf = args[1]
# read transcripts for filtering/processing
transcripts = gff.read_genes(ref_gtf, key_id='transcript_id')
# add unspliced single exon transcripts to hash
prerna_hash = set()
for tid in transcripts:
tx = transcripts[tid]
if len(tx.exons) == 1:
tx_key = (tx.chrom, tx.exons[0].start, tx.exons[0].end, tx.strand)
prerna_hash.add(tx_key)
# process transcripts
prerna_out = open(prerna_gtf, 'w')
prerna_index = 0
for tid in transcripts:
tx = transcripts[tid]
pre_start = tx.exons[0].start
pre_end = tx.exons[-1].end
pre_key = (tx.chrom, pre_start, pre_end, tx.strand)
# print exons
for i in range(len(tx.exons)):
cols = (tx.chrom, 'dk', 'exon', str(tx.exons[i].start),
str(tx.exons[i].end), '.', tx.strand, '.',
gff.kv_gtf(tx.kv))
print >> prerna_out, '\t'.join(cols)
# print prernas
if not pre_key in prerna_hash:
prerna_hash.add(pre_key)
pre_kv = copy.copy(tx.kv)
pre_kv['transcript_id'] = 'PRERNA%d' % prerna_index
pre_kv['transcript_type'] = 'prerna'
prerna_index += 1
cols = (tx.chrom, 'dk', 'exon', str(pre_start), str(pre_end), '.',
tx.strand, '.', gff.kv_gtf(pre_kv))
print >> prerna_out, '\t'.join(cols)
prerna_out.close()
if options.max_genes_overlapped != None:
# intersect with self and compute overlap sets
p = subprocess.Popen('intersectBed -wo -s -a %s -b %s' %
(prerna_gtf, prerna_gtf),
shell=True,
stdout=subprocess.PIPE)
tx_overlaps = {}
for line in p.stdout:
a = line.split('\t')
kv1 = gff.gtf_kv(a[8])
tid1 = kv1['transcript_id']
if tid1.startswith('PRERNA'):
gid1 = kv1['gene_id']
gid2 = gff.gtf_kv(a[17])['gene_id']
if gid1 != gid2:
tx_overlaps.setdefault(tid1, set()).add(gid2)
p.communicate()
# filter into a temp gtf
prerna_tmp_fd, prerna_tmp_file = tempfile.mkstemp()
prerna_out = open(prerna_tmp_file, 'w')
for line in open(prerna_gtf):
a = line.split('\t')
kv = gff.gtf_kv(a[8])
tid = kv['transcript_id']
if len(tx_overlaps.get(tid, [])) <= options.max_genes_overlapped:
print >> prerna_out, line,
prerna_out.close()
# rewrite temp to the final output
prerna_out = open(prerna_gtf, 'w')
for line in open(prerna_tmp_file):
print >> prerna_out, line,
prerna_out.close()
os.close(prerna_tmp_fd)
os.remove(prerna_tmp_file)
def compute_coverage(anchor_gff, event_files, mode, anchor_is_gtf, bins):
############################################
# initialize
############################################
coverage = initialize_coverage(anchor_gff, mode, anchor_is_gtf, bins)
if anchor_is_gtf:
# get transcript structures
transcripts = gff.read_genes(anchor_gff, key_id='transcript_id')
# compute lengths
transcript_lengths = {}
for tid in transcripts:
tx = transcripts[tid]
for exon in tx.exons:
transcript_lengths[tid] = transcript_lengths.get(
tid, 0) + exon.end - exon.start + 1
else:
transcripts = None
transcript_lengths = None
events = 0
for event_file in event_files:
print >> sys.stderr, 'Computing coverage for %s in %s' % (event_file,
anchor_gff)
############################################
# preprocess BAM/GFF
############################################
if event_file[-4:] == '.bam':
# count fragments and hash multi-mappers
multi_maps = {}
for aligned_read in pysam.Samfile(event_file, 'rb'):
try:
nh_tag = aligned_read.opt('NH')
except:
nh_tag = 1.0
if aligned_read.is_paired:
events += 0.5 / nh_tag
else:
events += 1.0 / nh_tag
if nh_tag > 1:
multi_maps[aligned_read.qname] = nh_tag
elif event_file[-4:] == '.gff':
for line in open(event_file):
events += 1
else:
print >> sys.stderr, 'Unknown event file format %s' % event_file
############################################
# intersect BAM w/ anchors
############################################
if event_file[-4:] == '.bam':
p = subprocess.Popen(
'intersectBed -split -wo -bed -abam %s -b %s' %
(event_file, anchor_gff),
shell=True,
stdout=subprocess.PIPE)
else:
p = subprocess.Popen('intersectBed -s -wo -a %s -b %s' %
(event_file, anchor_gff),
shell=True,
stdout=subprocess.PIPE)
for line in p.stdout:
a = line.split('\t')
if event_file[-4:] == '.bam':
rstart = int(a[1]) + 1 # convert back to 1-based gff from bed
rend = int(a[2])
rheader = a[3]
else:
rstart = int(a[3])
rend = int(a[4])
# because intersectBed screws up indels near endpoints
if rstart < rend:
if event_file[-4:] == '.bam':
acol = 12
else:
acol = 9
achrom = a[acol]
astart = int(a[acol + 3])
aend = int(a[acol + 4])
astrand = a[acol + 6]
if anchor_is_gtf:
anchor_id = gff.gtf_kv(a[acol + 8])['transcript_id']
else:
anchor_id = '%s:%d-%d' % (achrom, astart, aend)
# find where to increment
inc_start, inc_end = find_inc_coords(anchor_id, astart, aend,
astrand, rstart, rend,
mode, bins, transcripts,
transcript_lengths)
if inc_start != None:
if event_file[-4:] == '.bam':
# find multi-map number, which may require removing a suffix
if rheader in multi_maps:
mm = multi_maps[rheader]
else:
rheader_base = rheader[:rheader.rfind('/')]
if rheader_base in multi_maps:
mm = multi_maps[rheader_base]
else:
mm = 1.0
else:
mm = 1.0
# increment!
for i in range(inc_start, inc_end):
coverage[anchor_id][i] += 1.0 / mm
p.communicate()
return coverage, events
def main():
usage = 'usage: %prog [options] <ref_gtf>'
parser = OptionParser(usage)
#parser.add_option()
parser.add_option('-d',
dest='downstream',
type='int',
default=1000,
help='Downstream bp for promoters [Default: %default]')
parser.add_option(
'-f',
dest='fpkm_tracking',
help='Use cufflinks FPKM estimates to choose the most expressed isoform'
)
parser.add_option('-u',
dest='upstream',
type='int',
default=1000,
help='Upstream bp for promoters [Default: %default]')
(options, args) = parser.parse_args()
if len(args) != 1:
parser.error('Must provide reference GTF')
else:
ref_gtf = args[0]
g2t = gff.g2t(ref_gtf)
transcripts = gff.read_genes(ref_gtf)
source = open(ref_gtf).readline().split()[1]
if options.fpkm_tracking:
iso_fpkm_tracking = cufflinks.fpkm_tracking(options.fpkm_tracking)
for gene_id in g2t:
gene_transcripts = list(g2t[gene_id])
gene_strand = transcripts[gene_transcripts[0]].strand
if gene_strand not in ['+', '-']:
print >> sys.stderr, 'WARNING: %s discluded for lack of strand' % gene_id
continue
# choose TSS
if options.fpkm_tracking:
# find most expressed isoform
promoter_tid = gene_transcripts[0]
max_fpkm = stats.geo_mean([
1 + fpkm for fpkm in iso_fpkm_tracking.gene_expr(promoter_tid)
])
for transcript_id in gene_transcripts[1:]:
transcript_fpkm = stats.geo_mean([
1 + fpkm
for fpkm in iso_fpkm_tracking.gene_expr(transcript_id)
])
if math.isnan(max_fpkm) or transcript_fpkm > max_fpkm:
promoter_tid = transcript_id
max_fpkm = transcript_fpkm
# get isoform tss
if gene_strand == '+':
tss = transcripts[promoter_tid].exons[0].start
else:
tss = transcripts[promoter_tid].exons[-1].end
else:
# find most upstream tss
promoter_tid = gene_transcripts[0]
if gene_strand == '+':
upstream_tss = transcripts[promoter_tid].exons[0].start
else:
upstream_tss = transcripts[promoter_tid].exons[-1].end
for transcript_id in gene_transcripts[1:]:
if gene_strand == '+':
transcript_pos = transcripts[transcript_id].exons[0].start
if transcript_pos < upstream_tss:
promoter_tid = transcript_id
upstream_tss = transcript_pos
else:
transcript_pos = transcripts[transcript_id].exons[-1].end
if transcript_pos > upstream_tss:
promoter_tid = transcript_id
upstream_tss = transcript_pos
tss = upstream_tss
# print promoter from the tss
if gene_strand == '+':
if tss - options.upstream < 1:
print >> sys.stderr, 'WARNING: %s discluded for nearness to chromosome end' % gene_id
else:
tx = transcripts[promoter_tid]
cols = [
tx.chrom, source, 'promoter',
str(tss - options.upstream),
str(tss + options.downstream), '.', tx.strand, '.',
gff.kv_gtf(tx.kv)
]
print '\t'.join(cols)
else:
if tss - options.downstream < 1:
print >> sys.stderr, 'WARNING: %s discluded for nearness to chromosome end' % gene_id
else:
tx = transcripts[promoter_tid]
cols = [
tx.chrom, source, 'promoter',
str(tss - options.downstream),
str(tss + options.upstream), '.', tx.strand, '.',
gff.kv_gtf(tx.kv)
]
print '\t'.join(cols)
def get_splice_intervals(gtf_file, window):
intervals_5p = {}
intervals_3p = {}
genes = gff.read_genes(gtf_file)
for gid in genes:
g = genes[gid]
if len(g.exons) > 1:
if g.strand == "+":
# add first 5p site
exon = g.exons[0]
if not g.chrom in intervals_5p:
intervals_5p[g.chrom] = set()
intervals_5p[g.chrom].add((exon.end - window / 2, exon.end + window / 2, g.strand))
# process internal exons
for exon in g.exons[1:-1]:
# add 3p site
if not g.chrom in intervals_3p:
intervals_3p[g.chrom] = set()
intervals_3p[g.chrom].add((exon.start - window / 2, exon.start + window / 2, g.strand))
# add 5p site
if not g.chrom in intervals_5p:
intervals_5p[g.chrom] = set()
intervals_5p[g.chrom].add((exon.end - window / 2, exon.end + window / 2, g.strand))
# add last 3p site
exon = g.exons[-1]
if not g.chrom in intervals_3p:
intervals_3p[g.chrom] = set()
intervals_3p[g.chrom].add((exon.start - window / 2, exon.start + window / 2, g.strand))
else:
# add first 5p site
exon = g.exons[-1]
if not g.chrom in intervals_5p:
intervals_5p[g.chrom] = set()
intervals_5p[g.chrom].add((exon.end - window / 2, exon.end + window / 2, g.strand))
# process internal exons (in reverse order, but doesn't matter)
for exon in g.exons[1:-1]:
# add 3p site
if not g.chrom in intervals_3p:
intervals_3p[g.chrom] = set()
intervals_3p[g.chrom].add((exon.start - window / 2, exon.start + window / 2, g.strand))
# add 5p site
if not g.chrom in intervals_5p:
intervals_5p[g.chrom] = set()
intervals_5p[g.chrom].add((exon.end - window / 2, exon.end + window / 2, g.strand))
# add last 3p site
exon = g.exons[0]
if not g.chrom in intervals_3p:
intervals_3p[g.chrom] = set()
intervals_3p[g.chrom].add((exon.start - window / 2, exon.start + window / 2, g.strand))
# convert sets to sorted lists
for chrom in intervals_5p:
intervals_5p[chrom] = sorted(list(intervals_5p[chrom]))
intervals_3p[chrom] = sorted(list(intervals_3p[chrom]))
return intervals_5p, intervals_3p
