Used to truncate reads of lengths out of a given fasta filepython truncate_seq_lens.py X Y Z AwhereX is input fasta fileY is the minimum sequence lengthZ is the maximum sequence lengthA is output fasta file

truncate_seq_lens.py

#!/usr/bin/env python

""" Usage
python truncate_seq_lens.py X Y Z A
where
X is input fasta file
Y is the minimum sequence length (discards reads shorter than this)
Z is the maximum sequence length (discards reads longer than this)
A is target truncation length
B is output fasta file
"""
 
from sys import argv

from cogent.parse.fasta import MinimalFastaParser
 
f = open(argv[1], "U")
min_trunc_len = int(argv[2])
max_trunc_len = int(argv[3])
trunc_len = int(argv[4])
out_f = open(argv[5], "w")

 
for label,seq in MinimalFastaParser(f):
    if len(seq) < min_trunc_len or len(seq) > max_trunc_len:
        continue
    out_f.write(">%s\n%s\n" % (label, seq[0:trunc_len]))