SplitFastX.py

########################################################################################
## This file is a part of YAP package of scripts. https://github.com/shpakoo/YAP
## Distributed under the MIT license: http://www.opensource.org/licenses/mit-license.php
## Copyright (c) 2011-2013 Sebastian Szpakowski
########################################################################################

#################################################
##  Split FastX file into chunks of specified size
#################################################
import sys
from optparse import OptionParser
from Bio import SeqIO

_author="Sebastian Szpakowski"
_date="2012/03/29"
_version="Version 1"

#################################################
##      Classes
##

#################################################
##      Functions
##
    ################################################
    ### Read in a file and return a list of lines
    ###
def loadLines(x):
    try:
        fp = open(x, "r")
        cont=fp.readlines()
        fp.close()
        #print "%s line(s) loaded."  % (len(cont))
    except:
        cont=""
        #print "%s cannot be opened, does it exist? " % ( x )   
    return cont
#################################################
##      Arguments
##
parser = OptionParser()

parser.add_option("-i", "--input", dest="fn_input",
                  help="fastQ file name (or names, comma separated)", metavar="FILE")

parser.add_option("-c", "--chunk", dest="chunk_size", type=int,
                  help="put N sequences per output file", metavar="N")

parser.add_option("-f", "--format", dest="file_format", default="fasta",
                  help="list of names to remove", metavar="FILE")

(options, args) = parser.parse_args()

#################################################
##      Begin
##

counter_F = 0
outputs= list()
file_in = open(options.fn_input, "r")

for record in SeqIO.parse(file_in, options.file_format) :   
    outputs.append(record)
    if len(outputs) >= options.chunk_size:
        newfilename = "%s.%s.chunk.%s" % (".".join(options.fn_input.strip().split(".")[:-1]), counter_F, options.file_format)
        file_out = open(newfilename, "w")
        SeqIO.write(outputs, file_out, options.file_format) 
        file_out.close()
        outputs = list()
        counter_F += 1

if len(outputs)>0:
    newfilename = "%s.%s.chunk.%s" % (".".join(options.fn_input.strip().split(".")[:-1]), counter_F, options.file_format)
    file_out = open(newfilename, "w")
    SeqIO.write(outputs, file_out, options.file_format) 
    file_out.close()
        

file_in.close()
    

#################################################
##      Finish
#################################################