Specify an input fasta file and minimum length, e.g. python remove_short_reads.py seqs.fna 1300 > trimmed_reads.fna

remove_short_reads.py

#!/usr/bin/env python


from sys import argv

from cogent.parse.fasta import MinimalFastaParser

min_len = int(argv[2])

for label,seq in MinimalFastaParser(open(argv[1], "U")):
    if len(seq) >= min_len:
        print ">%s\n%s" % (label, seq)