Requires PyCogent installation. This should be present if you have QIIME installed. If you are using MacQIIME, initialize the environment by calling macqiime before using this script. Usage: python parse_bc_from_read_end.py X Y A B T/F Where: X is the input fasta file Y is the output fasta file A is the length of the forward barcode B is the len…

parse_bc_from_read_end.py

#!/usr/bin/env python

from sys import argv

from cogent.parse.fasta import MinimalFastaParser
from cogent import DNA

"""
Requires PyCogent installation. This should be present if you have QIIME 
installed. If you are using MacQIIME, initialize the environment by calling
macqiime before using this script.

Usage:
python parse_bc_from_read_end.py X Y A B T/F
Where:
X is the input fasta file
Y is the output fasta file
A is the length of the forward barcode
B is the length of the reverse barcode
T/F: pass "T" to reverse complement the reverse barcode, "F" to leave it as is
Example:
python parse_bc_from_read_end.py seqs.fna parsed_seqs.fna 8 8 T

This script will remove the last B bases of each read (assumed to be reverse
barcode) and put them immediately after the initial barcode (length is 
specified by the A parameter above). The final barcodes (combo of the forward
and reverse barcodes) can be listed as such in the mapping file for use with
split_libraries.py.

This script is designed for fasta reads, and assumes that the beginning and end
of the read are the barcodes. This script will not work if the barcodes are not
in these positions.
"""

input_fasta = open(argv[1], "U")
output_fasta = open(argv[2], "w")
f_bc_len = int(argv[3])
r_bc_len = int(argv[4])
if argv[5] == "T":
    rc = True
else:
    rc = False
    
for label, seq in MinimalFastaParser(input_fasta):
    curr_f_bc = seq[0:f_bc_len]
    if rc:
        curr_r_bc = DNA.rc(seq[-r_bc_len:])
    else:
        curr_r_bc = seq[-r_bc_len:]
    rest_of_seq = seq[f_bc_len:-r_bc_len]
    
    final_seq = curr_f_bc + curr_r_bc + rest_of_seq
    
    output_fasta.write(">%s\n%s\n" % (label, final_seq))