walterst

#!/usr/bin/env python

# USAGE: strip_primers_fastq.py Mapping_file input_fasta output_fasta log_filename

from sys import argv
from string import upper
from re import compile

from skbio.parse.sequences import parse_fastq
from skbio.sequence import DNA

brentp

"""                                                                                 
%prog some.fasta wanted-list.txt                                                    
"""                                                                                 
from Bio import SeqIO                                                               
import sys                                                                          
                                                                                    
wanted = [line.strip() for line in open(sys.argv[2])]                               
seqiter = SeqIO.parse(open(sys.argv[1]), 'fasta')                                    
SeqIO.write((seq for seq in seqiter if seq.id in wanted), sys.stdout, "fasta")