def load_gff(gff):
genes = defaultdict(list)
gene_exon_positions = defaultdict(lambda: defaultdict(tuple))
try:
with open(gff) as g:
for line in g:
if line.startswith('#') or 'contig' in line:
continue
feature = GFF(line)
gene_id = get_gene_attribute(feature, "ID")
if feature.featuretype == 'exon':
gene_exon_positions[feature.genename][gene_id] = (
feature.start, feature.end)
if feature.featuretype == 'CDS':
for exon in gene_exon_positions[feature.genename]:
e = gene_exon_positions[feature.genename][exon]
if e[0] <= feature.start <= e[1] and e[
0] <= feature.end <= e[1]:
gene_id = exon + "_CDS"
if gene_id is None:
print("No gene id for CDS found", feature, end="")
feature.id = gene_id
genes[feature.genename].append(feature)
except IOError:
print("Failed to load GFF file {}".format(gff))
sys.exit()
return genes
def load_gff(gff):
genes = defaultdict(list)
gene_exon_positions = defaultdict(lambda: defaultdict(tuple))
try:
with open(gff) as g:
for line in g:
if line.startswith('#') or 'contig' in line:
continue
feature = GFF(line)
gene_id = get_gene_attribute(feature, "ID")
if feature.featuretype == 'exon':
gene_exon_positions[feature.genename][gene_id] = (feature.start, feature.end)
if feature.featuretype == 'CDS':
for exon in gene_exon_positions[feature.genename]:
e = gene_exon_positions[feature.genename][exon]
if e[0] <= feature.start <= e[1] and e[0] <= feature.end <= e[1]:
gene_id = exon + "_CDS"
if gene_id is None:
print("No gene id for CDS found", feature, end="")
feature.id = gene_id
genes[feature.genename].append(feature)
except IOError:
print("Failed to load GFF file {}".format(gff))
sys.exit()
return genes
def load_crossmap(crossmapout):
genes = defaultdict(list)
gene_exon_positions = defaultdict(lambda: defaultdict(tuple))
try:
with open(crossmapout) as c:
for line in c:
cm = None
if 'fail' in line:
featureline = line.split('\tfail')[0]
if '->' in line:
featureline, cmline = line.split('\t->\t')
cm = GFF(cmline)
cm.attributes += ';Note=CrossMap'
feature = GFF(featureline)
feature.crossmap = cm
gene_id = get_gene_attribute(feature, "ID")
if feature.featuretype == 'exon':
gene_exon_positions[feature.genename][gene_id] = (
feature.start, feature.end)
if feature.featuretype == 'CDS':
for exon in gene_exon_positions[feature.genename]:
e = gene_exon_positions[feature.genename][exon]
if e[0] <= feature.start <= e[1] and e[
0] <= feature.end <= e[1]:
gene_id = exon + "_CDS"
if feature.crossmap: # Lose CrossMap features where the CDSs aren't the same length
cds_len = feature.end - feature.start + 1
cm_len = feature.crossmap.end - feature.crossmap.start + 1
if cds_len != cm_len:
feature.crossmap = None
if gene_id is None:
print("No gene id for CDS found", feature, end="")
feature.id = gene_id
genes[feature.genename].append(feature)
except IOError:
print("Failed to load CrossMap output {}".format(crossmapout))
sys.exit()
return genes
def load_crossmap(crossmapout):
genes = defaultdict(list)
gene_exon_positions = defaultdict(lambda: defaultdict(tuple))
try:
with open(crossmapout) as c:
for line in c:
cm = None
if 'fail' in line:
featureline = line.split('\tfail')[0]
if '->' in line:
featureline, cmline = line.split('\t->\t')
cm = GFF(cmline)
cm.attributes += ';Note=CrossMap'
feature=GFF(featureline)
feature.crossmap = cm
gene_id = get_gene_attribute(feature, "ID")
if feature.featuretype == 'exon':
gene_exon_positions[feature.genename][gene_id] = (feature.start, feature.end)
if feature.featuretype == 'CDS':
for exon in gene_exon_positions[feature.genename]:
e = gene_exon_positions[feature.genename][exon]
if e[0] <= feature.start <= e[1] and e[0] <= feature.end <= e[1]:
gene_id = exon + "_CDS"
if feature.crossmap: # Lose CrossMap features where the CDSs aren't the same length
cds_len = feature.end - feature.start + 1
cm_len = feature.crossmap.end - feature.crossmap.start + 1
if cds_len != cm_len:
feature.crossmap = None
if gene_id is None:
print("No gene id for CDS found", feature, end="")
feature.id = gene_id
genes[feature.genename].append(feature)
except IOError:
print("Failed to load CrossMap output {}".format(crossmapout))
sys.exit()
return genes