def read_rep_region(self, regionfile):
regions = HTSeq.GFF_Reader(regionfile, end_included=True)
rep_tree = IntervalTree()
for feature in regions:
iv = feature.iv
rep_tree.insert(iv, annotation='.')
return rep_tree
def read_rep_region(self, regionfile):
regions = HTSeq.GFF_Reader(regionfile, end_included=True)
rep_tree = IntervalTree()
for feature in regions:
iv = feature.iv
rep_tree.insert(iv, annotation='.')
return rep_tree
def selectGeneGtf(self, gtf_file):
# construct annotation tree
# new_gtf file contains only exon annotation
gtf = HTSeq.GFF_Reader(gtf_file, end_included=True)
annotation_tree = IntervalTree()
gtf_exon = []
for feature in gtf:
# Select only exon line
if feature.type == 'exon':
gtf_exon.append(feature.get_gff_line().split('\t'))
iv = feature.iv
try:
row = feature.attr
row['type'] = feature.type
except:
row = feature.get_gff_line()
annotation_tree.insert(iv, annotation=row)
gtf_exon_sorted = sorted(gtf_exon, key=lambda x: (x[0], int(x[3]), int(x[4])))
gtf_exon_sorted = ['\t'.join(s) for s in gtf_exon_sorted]
new_gtf = open(self.tmp_dir + "tmp_" + os.path.basename(gtf_file) + '.exon.sorted', 'w')
new_gtf.writelines(gtf_exon_sorted)
new_gtf.close()
return annotation_tree
def selectGeneGtf(self, gtf_file):
# construct annotation tree
# new_gtf file contains only exon annotation
gtf = HTSeq.GFF_Reader(gtf_file, end_included=True)
annotation_tree = IntervalTree()
gtf_exon = []
for feature in gtf:
# Select only exon line
if feature.type == 'exon':
gtf_exon.append(feature.get_gff_line().split('\t'))
iv = feature.iv
try:
row = feature.attr
row['type'] = feature.type
except:
row = feature.get_gff_line()
annotation_tree.insert(iv, annotation=row)
gtf_exon_sorted = sorted(gtf_exon,
key=lambda x: (x[0], int(x[3]), int(x[4])))
gtf_exon_sorted = ['\t'.join(s) for s in gtf_exon_sorted]
new_gtf = open(
self.tmp_dir + "tmp_" + os.path.basename(gtf_file) +
'.exon.sorted', 'w')
new_gtf.writelines(gtf_exon_sorted)
new_gtf.close()
return annotation_tree
def selectGeneGtf(self, gtf_file):
# select gene features for gtf or gff annotation file
gtf = HTSeq.GFF_Reader(gtf_file, end_included=True)
annotation_tree = IntervalTree()
for feature in gtf:
# Select only exon line
iv = feature.iv
try:
row = feature.attr
row['type'] = feature.type
except:
row = feature.get_gff_line()
annotation_tree.insert(iv, annotation=row)
return annotation_tree
def selectGeneGtf(self,gtf_file):
# select gene features for gtf or gff annotation file
gtf = HTSeq.GFF_Reader(gtf_file, end_included=True)
annotation_tree = IntervalTree()
for feature in gtf:
# Select only exon line
iv = feature.iv
try:
row = feature.attr
row['type'] = feature.type
except:
row = feature.get_gff_line()
annotation_tree.insert(iv, annotation=row)
return annotation_tree
def intersectcirc(self,
circ_file,
modified_gtf_file,
strand=True,
isStartBED=True):
# input the result file of print_start_end_file
input_bed_file = open(circ_file).readlines()
exon_gtf_file = HTSeq.GFF_Reader(modified_gtf_file, end_included=True)
gtf_exon_sorted = IntervalTree()
for feature in exon_gtf_file:
row = feature.attr
current_bed_interval = feature.iv
gtf_exon_sorted.insert(current_bed_interval, annotation=row)
circ_exon_set = {}
for bed_line in input_bed_file:
bed_field = bed_line.split('\t')
custom_exon_list = []
# we add 1bp in order for intersect to work correctly
# different case for start or end bed file
if isStartBED:
start = int(bed_field[1])
end = int(bed_field[1]) + 1
else:
start = int(bed_field[1]) - 1
end = int(bed_field[1])
# in order for the intersect to work, we need at least 1bp frame size
current_bed_interval = HTSeq.GenomicInterval(
bed_field[0], start, end, bed_field[5].strip())
# for later processing however, we again need the "0" bp frame window
insert_bed_interval = HTSeq.GenomicInterval(
bed_field[0], int(bed_field[1]), int(bed_field[2]),
bed_field[5].strip())
# extract all customs exons
gtf_exon_sorted.intersect(
current_bed_interval, lambda x: custom_exon_list.append(
x.annotation['custom_exon_id']))
if custom_exon_list: # if we found one or more custom exons
for custom_exon in custom_exon_list: # go through the list
circ_exon_set.setdefault(insert_bed_interval, set()).add(
custom_exon) # and add them to the set
# return the filled set
return circ_exon_set
def intersectcirc(self, circ_file, modified_gtf_file, strand=True, isStartBED=True):
# input the result file of print_start_end_file
input_bed_file = open(circ_file).readlines()
exon_gtf_file = HTSeq.GFF_Reader(modified_gtf_file, end_included=True)
gtf_exon_sorted = IntervalTree()
for feature in exon_gtf_file:
row = feature.attr
current_bed_interval = feature.iv
gtf_exon_sorted.insert(current_bed_interval, annotation=row)
circ_exon_set = {}
for bed_line in input_bed_file:
bed_field = bed_line.split('\t')
custom_exon_list = []
# we add 1bp in order for intersect to work correctly
# different case for start or end bed file
if isStartBED:
start = int(bed_field[1])
end = int(bed_field[1]) + 1
else:
start = int(bed_field[1]) - 1
end = int(bed_field[1])
# in order for the intersect to work, we need at least 1bp frame size
current_bed_interval = HTSeq.GenomicInterval(bed_field[0],
start,
end,
bed_field[5].strip()
)
# for later processing however, we again need the "0" bp frame window
insert_bed_interval = HTSeq.GenomicInterval(bed_field[0],
int(bed_field[1]),
int(bed_field[2]),
bed_field[5].strip()
)
# extract all customs exons
gtf_exon_sorted.intersect(current_bed_interval,
lambda x: custom_exon_list.append(x.annotation['custom_exon_id'])
)
if custom_exon_list: # if we found one or more custom exons
for custom_exon in custom_exon_list: # go through the list
circ_exon_set.setdefault(insert_bed_interval, set()).add(custom_exon) # and add them to the set
# return the filled set
return circ_exon_set
