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Fix repeatmasker GFF2Bed out of sort issue #27

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merged 1 commit into from
Dec 20, 2022
Merged

Fix repeatmasker GFF2Bed out of sort issue #27

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9 changes: 8 additions & 1 deletion src/telr/TELR_te.py
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Original file line number Diff line number Diff line change
Expand Up @@ -447,7 +447,8 @@ def gff3tobed(gff, bed):
)
sys.exit(1)
break
with open(bed, "w") as output, open(gff, "r") as input:
bed_tmp = bed + ".tmp"
with open(bed_tmp, "w") as output, open(gff, "r") as input:
for line in input:
if "#" not in line:
entry = line.replace("\n", "").split("\t")
Expand All @@ -459,6 +460,12 @@ def gff3tobed(gff, bed):
[entry[0], str(int(entry[3]) - 1), entry[4], family, ".", entry[6]]
)
output.write(out_line + "\n")

# sort BED file
command = "bedtools sort -i " + bed_tmp
with open(bed, "w") as output:
subprocess.call(command, shell=True, stdout=output)
os.remove(bed_tmp)


def parse_rm_out(rm_gff, gff3):
Expand Down