extract_bcs_from_fastq_ends.py

#!/usr/bin/env python

""" Usage
python extract_bcs_from_fastq_ends.py X Y Z A B C D E
Where
X: input fastq file with barcodes at the beginning and ends of the reads 
Y: output fastq barcodes file 
Z: output reads fastq file (with barcodes removed) 
A: length of forward barcode (int) 
B: length of reverse barcode (int) 
C: True/False flag to reverse complement the forward barcode 
D: True/False flag to reverse complement the reverse barcode
E: True/False switch order of barcodes (False-order is barcode at start of
 the read followed by barcode at end of read, True-order is barcode at end of
 read followed by barcode at the beginning of the read).
"""
 
from sys import argv
 
from cogent.parse.fastq import MinimalFastqParser
from cogent import DNA
 
f = open(argv[1], "U")
bc_out = open(argv[2], "w")
read_out = open(argv[3], "w")
 
f_barcode_size = int(argv[4])
r_barcode_size = int(argv[5])

rc_f_bc = argv[6]
if rc_f_bc == "True":
    rc_f_bc = True
elif rc_f_bc == "False":
    rc_f_bc = False
else:
    raise ValueError,("Fifth parameter must either be True or False")

rc_r_bc = argv[7]
if rc_r_bc == "True":
    rc_r_bc = True
elif rc_r_bc == "False":
    rc_r_bc = False
else:
    raise ValueError,("Sixth parameter must either be True or False")
    
switch_bc_order = argv[8]
if switch_bc_order == "True":
    switch_bc_order = True
elif switch_bc_order == "False":
    switch_bc_order = False
else:
    raise ValueError,("Seventh parameter must either be True or False")

for data in MinimalFastqParser(f, strict=False):
   curr_label = data[0].strip()
   
   curr_f_bc_read = data[1].strip()[0:f_barcode_size]
   curr_read = data[1].strip()[f_barcode_size:-r_barcode_size]
   curr_r_bc_read = data[1].strip()[-r_barcode_size:]
   
   if rc_f_bc:
      curr_f_bc_read = DNA.rc(curr_f_bc_read)
   if rc_r_bc:
      curr_r_bc_read = DNA.rc(curr_r_bc_read)
      
   curr_f_bc_qual = data[2].strip()[0:f_barcode_size]
   curr_qual = data[2].strip()[f_barcode_size:-r_barcode_size]
   curr_r_bc_qual = data[2].strip()[-r_barcode_size:]
   
   if rc_f_bc:
      curr_f_bc_qual = curr_f_bc_qual[::-1]
   if rc_r_bc:
      curr_r_bc_qual = curr_r_bc_qual[::-1]
   
   bc_out.write("@%s\n" % curr_label)
   if switch_bc_order:
       final_bc_read = curr_r_bc_read + curr_f_bc_read
       final_bc_qual = curr_r_bc_qual + curr_f_bc_qual
   else:
       final_bc_read = curr_f_bc_read + curr_r_bc_read
       final_bc_qual = curr_f_bc_qual + curr_r_bc_qual
   bc_out.write("%s\n" % final_bc_read)
   bc_out.write("+\n")
   bc_out.write("%s\n" % final_bc_qual)
   read_out.write("@%s\n" % curr_label)
   read_out.write("%s\n" % curr_read)
   read_out.write("+\n")
   read_out.write("%s\n" % curr_qual)