def get_non_absent_ref_tes(te_gff, absence_bed, sample, out, log):
insertions = []
tmp_gff = out + "/tmp.ref_nonabs.gff"
command = ["bedtools", "subtract", "-A", "-a", te_gff, "-b", absence_bed]
mccutils.run_command_stdout(command, tmp_gff, log=log)
with open(tmp_gff, "r") as gff:
for line in gff:
if "#" not in line:
line = line.replace(";", "\t")
split_line = line.split("\t")
insert = output.Insertion(output.Temp())
insert.chromosome = split_line[0]
insert.start = int(split_line[3])
insert.end = int(split_line[4])
insert.name = split_line[9].split(
"=")[1] + "|reference|NA|" + sample + "|temp|nonab|"
insert.strand = split_line[6]
insert.type = "reference"
insertions.append(insert)
mccutils.remove(tmp_gff)
return insertions
def read_insertion_summary(infile, sample):
insertions = []
with open(infile, "r") as inf:
for x, line in enumerate(inf):
if x > 0:
insert = output.Insertion(output.Temp())
split_line = line.split("\t")
if len(split_line) == 14:
insert.chromosome = split_line[0]
insert.start = int(split_line[1]) - 1
insert.end = int(split_line[2])
insert.family = split_line[3]
insert.name = insert.family + "|non-reference|" + split_line[
7] + "|" + sample + "|temp|"
if "antisense" in split_line[4]:
insert.strand = "-"
else:
insert.strand = "+"
insert.support_info.support['class'].value = split_line[5]
insert.support_info.support['variantsupport'].value = int(
float(split_line[6]))
insert.support_info.support['frequency'].value = float(
split_line[7])
insert.support_info.support['junction1'].value = int(
split_line[8])
insert.support_info.support[
'junction1support'].value = int(split_line[9])
insert.support_info.support['junction2'].value = int(
split_line[10])
insert.support_info.support[
'junction2support'].value = int(split_line[11])
insert.support_info.support[
'fiveprimesupport'].value = int(float(split_line[12]))
insert.support_info.support[
'threeprimesupport'].value = int(
float(split_line[13].replace("\n", "")))
insert.type = "non-reference"
if insert.end >= insert.start and insert.end > 0 and insert.start > -1:
# if split read, use junction positions as start and end
if insert.support_info.support[
'junction1support'].value > 0 and insert.support_info.support[
'junction2support'].value > 0:
insert.start = insert.support_info.support[
'junction1'].value
insert.end = insert.support_info.support[
'junction2'].value
insert.name = insert.name + "sr|"
# read pair
else:
insert.name = insert.name + "rp|"
insertions.append(insert)
else:
print(
"<TEMP POST> Omitting malformed line from insertion summary results:",
line)
else:
print(
"<TEMP POST> Omitting malformed line from insertion summary results:",
line)
return insertions