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#!/usr/bin/python
import sys, argparse
from pbsuite.utils.setupLogging import *
USAGE = "Split input.[fastq|fasta] file into N subfiles"
parser = argparse.ArgumentParser(description=USAGE, \
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument("input", metavar="INPUT", \
help="File to be split")
parser.add_argument("nSplits", metavar="N", type=int, \
help="Number of splits to create")
parser.add_argument("-o", "--outPrefix", default=None,\
help="Prefix for output files")
#parser.add_argument("-m", "--multiline", action="store_true",\
#help="Input file is expected to be multiline per entry")
args = parser.parse_args()
format = 0
if args.input.lower().endswith(".fastq"):
format = 4
suffix = ".fastq"
elif args.input.lower().endswith(".fasta"):
format = 2
suffix = ".fasta"
if not format:
logging.error("Input must be .fastq or .fasta")
exit(0)
if args.outPrefix is None:
args.outPrefix = args.input[:len(".fasta")]
outFiles = []
for i in range(args.nSplits):
outFiles.append(open(args.outPrefix + str(i) + suffix, 'w'))
fh = open(args.input, 'r')
index = 0
while True:
name = fh.readline()
seq = fh.readline()
if name == "":
break
outFiles[index].write(name + seq)
if format == 4:
#plus
outFiles[index].write(fh.readline())
#qual
outFiles[index].write(fh.readline())
index += 1#I could mod here..
if index >= args.nSplits:
index = 0
for f in outFiles:
f.close()
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