'''

cgat_script_template.py - template for CGAT scripts

====================================================

:Author:

:Release: $Id$

:Date: |today|

:Tags: Python

Purpose

-------

Extract UMI barcode from a read and add it to the read name, leaving

any sample barcode in place. Can deal with paired end reads and UMIs

split across the paired ends

Options

-------

--read2-in, --read2-out

Optionally a file with read pairs can be provided. The UMI will

be added to the read2 read name as well. Assumes that reads

are in the same order. read2-out specifies the output file.

--split-barcode

By default the UMI is assumed to be on the first read. Use this

option if the UMI is contained on both reads and specify the

pattern of the barcode/UMI on the second read using the option

``--bc-pattern2``

--bc-pattern

Use this option to specify the format of the UMI/barcode. Use Ns to

represent the random positions and Xs to indicate the bc positions.

Bases with Ns will be extracted and added to the read name. Remaining

bases, marked with an X will be reattached to the read.

E.g. If the pattern is NNXXNN,

Then the read:

@HISEQ:87:00000000 read1

AAGGTTGCTGATTGGATGGGCTAG

DA1AEBFGGCG01DFH00B1FF0B

+

will become:

@HISEQ:87:00000000_AATT read1

GGGCTGATTGGATGGGCTAG

1AFGGCG01DFH00B1FF0B

+

--bc-pattern2

Use this option to specify the format of the UMI/barcode for

the second read pair if required. If --bc-pattern2 is not

supplied, this defaults to the same pattern as --bc-pattern

--3prime

By default the barcode is assumed to be on the 5' end of the read, but

use this option to sepecify that it is on the 3' end instead

-L

Specify a log file to retain logging information and final statistics

--supress-stats

Supress logging of summary statistics

Usage:

------

For single ended reads

python extract_umi.py --bc-pattern=[PATTERN] -L extract.log [OPTIONS]

reads from stdin and outputs to stdout.

For paired end reads:

python extract_umi.py --bc-pattern=[PATTERN] --read2-in=[FASTQIN] --read2-out=[FASTQOUT] -L extract.log [OPTIONS]

reads end one from stdin and end two from FASTQIN and outputs end one to stdin

and end two to FASTQOUT.

Command line options

--------------------

'''

import sys

import CGAT.Experiment as E

import CGAT.Fastq as Fastq

import CGAT.IOTools as IOTools

def addUMItoIdentifier(read, UMI):

return identifier

class Extractor:

return read1

def main(argv=None):

E.Stop()

if __name__ == "__main__":

sys.exit(main(sys.argv))