/usr/bin/remove_dup_ctg is in falconkit 0.1.3+20140820-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
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import pbcore.io
import sys
"""nucmer -maxmatch all_tigs.fa all_tigs.fa -p all_tigs_self >& /dev/null"""
"""show-coords -o -H -T all_tigs_self.delta | grep CONTAINS | awk '$7>96' | awk '{print $9}' | sort -u > all_tigs_duplicated_ids"""
id_to_remove = set()
with open("all_tigs_duplicated_ids") as f:
for l in f:
l = l.strip().split("-")
major, minor = l[:2]
id_to_remove.add ( (major, minor) )
f = pbcore.io.FastaReader("all_tigs.fa")
with open("a-tigs_nodup.fa", "w") as f_out:
for r in f:
major, minor = r.name.split()[0].split("-")[:2]
if minor == "0000":
continue
if (major, minor) in id_to_remove:
continue
if len(r.sequence) < 500:
continue
print >>f_out, ">"+r.name
print >>f_out, r.sequence
f = pbcore.io.FastaReader("primary_tigs_c.fa")
with open("p-tigs_nodup.fa", "w") as f_out:
for r in f:
major, minor = r.name.split()[0].split("_")[:2]
if (major, "0000") in id_to_remove:
continue
if len(r.sequence) < 500:
continue
print >>f_out, ">"+r.name
print >>f_out, r.sequence
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