def intersect_clusters_with_gff(logger,
clusters_fname,
gff_filenames,
output_dir):
"""
Intersect CLIP clusters with a set of GFF filenames
(e.g. GFFs containing events.)
"""
event_clusters_fnames = []
logger.info("Intersecting clusters %s with GFFs.." \
%(clusters_fname))
for gff_fname in gff_filenames:
if not os.path.isfile(gff_fname):
logger.critical("Cannot find events GFF file %s" \
%(gff_fname))
continue
gff_label = os.path.basename(utils.trim_gff_ext(gff_fname))
event_clusters_fname = \
os.path.join(output_dir,
"%s.clusters.bed" %(gff_label))
logger.info(" - Processing GFF %s" %(gff_label))
# Intersect the clusters for this sample with each
# GFF file
intersectBed_cmd = \
"%s -a %s -b %s -loj -f 1 > %s" \
%(bedtools_utils.intersectBed_path,
clusters_fname,
gff_fname,
event_clusters_fname)
if os.path.isfile(event_clusters_fname):
logger.info("Found %s, skipping.." %(event_clusters_fname))
event_clusters_fnames.append(event_clusters_fname)
continue
logger.info(" - Executing: %s" %(intersectBed_cmd))
ret_val = os.system(intersectBed_cmd)
if ret_val != 0:
logger.critical("Cannot intersect clusters with %s" \
%(gff_fname))
else:
event_clusters_fnames.append(event_clusters_fname)
return event_clusters_fnames
def intersect_clusters_with_gff(logger, clusters_fname, gff_filenames,
output_dir):
"""
Intersect CLIP clusters with a set of GFF filenames
(e.g. GFFs containing events.)
"""
event_clusters_fnames = []
logger.info("Intersecting clusters %s with GFFs.." \
%(clusters_fname))
for gff_fname in gff_filenames:
if not os.path.isfile(gff_fname):
logger.critical("Cannot find events GFF file %s" \
%(gff_fname))
continue
gff_label = os.path.basename(utils.trim_gff_ext(gff_fname))
event_clusters_fname = \
os.path.join(output_dir,
"%s.clusters.bed" %(gff_label))
logger.info(" - Processing GFF %s" % (gff_label))
# Intersect the clusters for this sample with each
# GFF file
intersectBed_cmd = \
"%s -a %s -b %s -loj -f 1 > %s" \
%(bedtools_utils.intersectBed_path,
clusters_fname,
gff_fname,
event_clusters_fname)
if os.path.isfile(event_clusters_fname):
logger.info("Found %s, skipping.." % (event_clusters_fname))
event_clusters_fnames.append(event_clusters_fname)
continue
logger.info(" - Executing: %s" % (intersectBed_cmd))
ret_val = os.system(intersectBed_cmd)
if ret_val != 0:
logger.critical("Cannot intersect clusters with %s" \
%(gff_fname))
else:
event_clusters_fnames.append(event_clusters_fname)
return event_clusters_fnames
def add_introns_to_gff(gff_filename, output_dir):
"""
Add 'intron' entries to GFF.
"""
output_basename = \
utils.trim_gff_ext(os.path.basename(gff_filename))
ext_to_use = os.path.basename(gff_filename).rsplit(".", 1)[1]
output_filename = \
os.path.join(output_dir,
"%s.with_introns.%s" %(output_basename,
ext_to_use))
print "Adding introns to GFF..."
print " - Input: %s" %(gff_filename)
print " - Output: %s" %(output_filename)
if os.path.isfile(output_filename):
print "Found file %s, skipping.." %(output_filename)
return output_filename
gff_out = miso_gff_utils.Writer(open(output_filename, "w"))
gff_db = miso_gff_utils.GFFDatabase(from_filename=gff_filename,
reverse_recs=True)
t1 = time.time()
genes = gene_utils.load_genes_from_gff(gff_filename)
for gene_id in genes:
gene_info = genes[gene_id]
gene_tree = gene_info["hierarchy"]
gene_obj = gene_info["gene_object"]
gene_rec = gene_tree[gene_id]["gene"]
# Write the GFF record
gff_out.write(gene_rec)
# Write out the mRNAs, their exons, and then
# input the introns
for mRNA in gene_obj.isoforms:
mRNA_id = mRNA.label
curr_mRNA = gene_tree[gene_id]["mRNAs"][mRNA_id]
gff_out.write(curr_mRNA["record"])
# Write out the exons
curr_exons = gene_tree[gene_id]["mRNAs"][mRNA_id]["exons"]
for exon in curr_exons:
gff_out.write(curr_exons[exon]["record"])
# Now output the introns
for isoform in gene_obj.isoforms:
intron_coords = []
for first_exon, second_exon in zip(isoform.parts,
isoform.parts[1::1]):
# Intron start coordinate is the coordinate right after
# the end of the first exon, intron end coordinate is the
# coordinate just before the beginning of the second exon
intron_start = first_exon.end + 1
intron_end = second_exon.start - 1
if intron_start >= intron_end:
continue
intron_coords.append((intron_start, intron_end))
# Create record for this intron
intron_id = "%s:%d-%d:%s.intron" \
%(gene_obj.chrom,
intron_start,
intron_end,
gene_obj.strand)
intron_rec = \
miso_gff_utils.GFF(gene_obj.chrom, gene_rec.source, "intron",
intron_start, intron_end,
strand=gene_obj.strand,
attributes={"ID": [intron_id],
"Parent": [isoform.label]})
gff_out.write(intron_rec)
t2 = time.time()
print "Addition took %.2f minutes." %((t2 - t1)/60.)
