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#!/usr/bin/python3
import sys, os
from pbcore.io import FastaIO
def run(reader, writer, lookupfile):
with open (lookupfile,'w') as f:
for i,record in enumerate(reader):
seq_length = len(record.sequence)
zmw = i+1
old_header=record.header
if seq_length < 30:
new_header = 'Deleted'
f.write(old_header+'\t'+new_header+'\n')
continue
#bounds = record.header.split('/')[-1]
#start, end = [int(k) for k in bounds.split('_')]
start = 0
new_end = start + seq_length
new_header = "m000_000/{zmw}/{start}_{end}".format(zmw=zmw, start=start, end=new_end)
f.write(old_header+'\t'+new_header+'\n')
writer.writeRecord(new_header, record.sequence)
def main(iname, ofile, lookupfile):
reader = FastaIO.FastaReader(iname)
writer = FastaIO.FastaWriter(ofile)
run(reader, writer,lookupfile)
if __name__ == '__main__':
iname, oname, lookupfile = sys.argv[1:4]
ofile = open(oname, 'w')
try:
main(iname, ofile, lookupfile)
except:
# clean up (for make)
ofile.close()
os.unlink(oname)
raise
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