This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
#!/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 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
""" | |
%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") |