# This script splits libraries obtained from sequencing with different markers. I.e. one library - one marker.

# You will have to provide read ids where another marker start. Read ids should be provided in text file: one line - one read id.

# For now you should provide only one stop read id, i.e. when the program sees this id, it stops and writes content into provided

# output file.

from Bio.Seq import Seq

from Bio import SeqIO

from Bio.Alphabet import generic_dna

import sys

def split_by_marker1(infile, outfile, id) :

handle = open(infile, "rU")

records = []

for record in SeqIO.parse(handle, "fastq") :

if record.id == id :

break

records.append(record)

handle.close()

# Writing output

handle = open(outfile, "w")

SeqIO.write(records, handle, "fastq")

def split_by_marker2(infile, outfile, id) :

handle = open(infile, "rU")

records = []

flag = False

for record in SeqIO.parse(handle, "fastq") :

if record.id == id :

#break

flag = True

if flag == True :

records.append(record)

handle.close()

# Writing output

handle = open(outfile, "w")

SeqIO.write(records, handle, "fastq")

def rev2fwd(infile, outfile) :

handle = open(infile, "rU")

records = []

revcomp = False

for record in SeqIO.parse(handle, "fastq") :

if record.id == "SRR072221.58746" :

break

if record.id == "SRR072221.29034" :

revcomp = True

if revcomp == True :

new_record = record.reverse_complement()

new_record.id = record.id

new_record.description = record.description

records.append(new_record)

else :

records.append(record)

handle.close()

# Writing output

handle = open(outfile, "w")

SeqIO.write(records, handle, "fastq")

def main() :

outfile = sys.argv[-2]

infile = sys.argv[-3]

read_id = sys.argv[-1]

split_by_marker2(infile, outfile, read_id)

if __name__ == '__main__':

main()