def main():
usage = 'usage: %prog [options] <gene/transcript id>'
parser = OptionParser(usage)
parser.add_option('-c', dest='cuff_dir', default='%s/research/common/data/lncrna'%os.environ['HOME'], help='Cufflinks output directory with .fpkm_tracking files [Default: %default]')
parser.add_option('-l', dest='lnc_gtf', default='%s/research/common/data/lncrna/lnc_catalog.gtf'%os.environ['HOME'], help='lncRNA catalog gtf file [Default: %default]')
parser.add_option('-t', dest='transcript_expr', default=False, action='store_true', help='Return transcript expression rather than gene [Default: %default]')
(options,args) = parser.parse_args()
if options.transcript_expr:
cuff = cufflinks.fpkm_tracking('%s/isoforms.fpkm_tracking' % options.cuff_dir)
if args[0].find('XLOC') != -1:
trans_ids = set()
for line in open(options.lnc_gtf):
a = line.split('\t')
kv = gff.gtf_kv(a[8])
if kv['gene_id'] == args[0]:
trans_ids.add(kv['transcript_id'])
else:
trans_ids = [args[0]]
for trans_id in trans_ids:
print '%s:' % trans_id
cuff.gene_expr_print(trans_id)
else:
cuff = cufflinks.fpkm_tracking('%s/genes.fpkm_tracking' % options.cuff_dir)
if args[0].find('XLOC') != -1:
gene_id = args[0]
else:
t2g = gff.t2g(options.lnc_gtf)
gene_id = t2g[args[0]]
cuff.gene_expr_print(gene_id)
def main():
usage = 'usage: %prog [options] <gff file>'
parser = OptionParser(usage)
parser.add_option('-c',
dest='cons_dir',
default='%s/research/common/data/phylop' %
os.environ['HOME'],
help='Conservation directory [Default: %default]')
parser.add_option(
'-l',
dest='lncrna',
action='store_true',
default=False,
help=
'Use the lncRNA specific file to speed things up [Default: %default]')
(options, args) = parser.parse_args()
if len(args) != 1:
parser.error('Must provide gff file to intersect')
else:
gff_file = args[0]
t2g = gff.t2g(gff_file)
# build interval trees
lnc_lengths = {}
chr_features = {}
interval2lnc = {}
lnc_cons = {}
for line in open(gff_file):
a = line.split('\t')
chrom = a[0]
start = int(a[3])
end = int(a[4])
tid = gff.gtf_kv(a[8])['transcript_id']
align = (chrom, start, end)
lnc_cons[tid] = []
lnc_lengths[tid] = lnc_lengths.get(tid, 0) + (end - start + 1)
if interval2lnc.has_key(align):
interval2lnc[align].add(tid)
else:
interval2lnc[align] = set([tid])
chr_features.setdefault(chrom, IntervalTree()).insert_interval(
Interval(start, end))
# process overlapping chromosome blocks
if options.lncrna:
lnc_wig = glob.glob('%s/lnc_catalog.*wigFix*' % options.cons_dir)[0]
process_file(chr_features, interval2lnc, lnc_cons, lnc_wig)
else:
for cons_file in glob.glob('%s/chr*' % options.cons_dir):
process_file(chr_features, interval2lnc, lnc_cons, cons_file)
# print table
for tid in lnc_lengths:
cons_len = len(lnc_cons[tid])
cons_cov = float(cons_len) / lnc_lengths[tid]
if cons_len == 0:
cons_mean = 0.0
cons_median = 0.0
cons_pos = 0.0
cons_neg = 0.0
else:
cons_mean = stats.mean(lnc_cons[tid])
cons_median = stats.median(lnc_cons[tid])
cons_pos = len([c
for c in lnc_cons[tid] if c > 1]) / float(cons_len)
cons_neg = len([c
for c in lnc_cons[tid] if c < 1]) / float(cons_len)
cols = (tid, t2g[tid], lnc_lengths[tid], cons_cov, cons_mean,
cons_median, cons_neg, cons_pos)
print '%-15s %-15s %7d %9.4f %9.4f %9.4f %9.4f %9.4f' % cols
def main():
usage = 'usage: %prog [options] <gff file>'
parser = OptionParser(usage)
parser.add_option('-c', dest='cons_dir', default='%s/research/common/data/phylop' % os.environ['HOME'], help='Conservation directory [Default: %default]')
parser.add_option('-l', dest='lncrna', action='store_true', default=False, help='Use the lncRNA specific file to speed things up [Default: %default]')
(options,args) = parser.parse_args()
if len(args) != 1:
parser.error('Must provide gff file to intersect')
else:
gff_file = args[0]
t2g = gff.t2g(gff_file)
# build interval trees
lnc_lengths = {}
chr_features = {}
interval2lnc = {}
lnc_cons = {}
for line in open(gff_file):
a = line.split('\t')
chrom = a[0]
start = int(a[3])
end = int(a[4])
tid = gff.gtf_kv(a[8])['transcript_id']
align = (chrom,start,end)
lnc_cons[tid] = []
lnc_lengths[tid] = lnc_lengths.get(tid,0) + (end-start+1)
if interval2lnc.has_key(align):
interval2lnc[align].add(tid)
else:
interval2lnc[align] = set([tid])
chr_features.setdefault(chrom, IntervalTree()).insert_interval(Interval(start,end))
# process overlapping chromosome blocks
if options.lncrna:
lnc_wig = glob.glob('%s/lnc_catalog.*wigFix*' % options.cons_dir)[0]
process_file(chr_features, interval2lnc, lnc_cons, lnc_wig)
else:
for cons_file in glob.glob('%s/chr*' % options.cons_dir):
process_file(chr_features, interval2lnc, lnc_cons, cons_file)
# print table
for tid in lnc_lengths:
cons_len = len(lnc_cons[tid])
cons_cov = float(cons_len) / lnc_lengths[tid]
if cons_len == 0:
cons_mean = 0.0
cons_median = 0.0
cons_pos = 0.0
cons_neg = 0.0
else:
cons_mean = stats.mean(lnc_cons[tid])
cons_median = stats.median(lnc_cons[tid])
cons_pos = len([c for c in lnc_cons[tid] if c > 1]) / float(cons_len)
cons_neg = len([c for c in lnc_cons[tid] if c < 1]) / float(cons_len)
cols = (tid, t2g[tid], lnc_lengths[tid], cons_cov, cons_mean, cons_median, cons_neg, cons_pos)
print '%-15s %-15s %7d %9.4f %9.4f %9.4f %9.4f %9.4f' % cols
def main():
usage = 'usage: %prog [options] <ref gtf> <merged gtf>'
parser = OptionParser(usage)
(options,args) = parser.parse_args()
if len(args) != 2:
parser.error(usage)
else:
ref_gtf = args[0]
merged_gtf = args[1]
# get mappings
ref_t2g = gff.t2g(ref_gtf)
merged_t2g = gff.t2g(merged_gtf)
merged_g2t = gff.g2t(merged_gtf)
# hash gene_name's by tid
ref_gid_names = {}
for line in open(ref_gtf):
a = line.split('\t')
kv = gff.gtf_kv(a[8])
if 'gene_name' in kv:
ref_gid_names[kv['gene_id']] = kv['gene_name']
# hash merged lines by tid
merged_tid_lines = {}
for line in open(merged_gtf):
a = line.split('\t')
tid = gff.gtf_kv(a[8])['transcript_id']
merged_tid_lines.setdefault(tid,[]).append(line)
# intialize orphan gene_id
orphan_num = 1
for mgene_id in merged_g2t:
# count reference genes
ref_genes = set()
for tid in merged_g2t[mgene_id]:
if tid in ref_t2g:
ref_genes.add(ref_t2g[tid])
# if no known genes, leave it alone
if len(ref_genes) == 0:
for tid in merged_g2t[mgene_id]:
print ''.join(merged_tid_lines[tid]),
# if known gene, set gene_id to it
elif len(ref_genes) == 1:
new_gene_id = list(ref_genes)[0]
for tid in merged_g2t[mgene_id]:
for line in merged_tid_lines[tid]:
a = line.split('\t')
kv = gff.gtf_kv(a[8])
kv['gene_id'] = new_gene_id
if new_gene_id in ref_gid_names:
kv['gene_name'] = ref_gid_names[new_gene_id]
a[8] = gff.kv_gtf(kv)
print '\t'.join(a)
# if two known genes were combined, fix it
elif len(ref_genes) > 1:
# compute transcript overlaps and build overlap graph
tid_overlap_graph = make_overlap_graph(mgene_id, merged_g2t, merged_tid_lines)
# map each new transcript to the ref gene_id's overlapped
tid_ref_genes = {}
for (tid1,tid2) in tid_overlap_graph.edges():
if tid1 in ref_t2g and tid2 not in ref_t2g:
tid_ref_genes.setdefault(tid2,set()).add(ref_t2g[tid1])
elif tid1 not in ref_t2g and tid2 in ref_t2g:
tid_ref_genes.setdefault(tid1,set()).add(ref_t2g[tid2])
# remove new transcripts overlapping multiple ref gene_id's
for tid in tid_ref_genes:
if len(tid_ref_genes[tid]) > 1:
print >> sys.stderr, 'Removing %s' % tid
tid_overlap_graph.remove_node(tid)
# remove edges connecting separate reference genes
for (tid1,tid2) in tid_overlap_graph.edges():
if tid1 in ref_t2g and tid2 in ref_t2g and ref_t2g[tid1] != ref_t2g[tid2]:
tid_overlap_graph.remove_edge(tid1,tid2)
# map to new gene_id's; missing means eliminate transcript
tid_new_gid, orphan_num = map_new_gid(tid_overlap_graph, orphan_num, ref_t2g)
for tid in merged_g2t[mgene_id]:
if tid in tid_new_gid:
for line in merged_tid_lines[tid]:
a = line.split('\t')
kv = gff.gtf_kv(a[8])
kv['gene_id'] = tid_new_gid[tid]
if tid_new_gid[tid] in ref_gid_names:
kv['gene_name'] = ref_gid_names[tid_new_gid[tid]]
a[8] = gff.kv_gtf(kv)
print '\t'.join(a)