Merge FASTQ files from multiple lanes.

merge_lanes.py

#!/usr/bin/env python
# encoding: utf8
"""
merge_lanes.py
Kamil Slowikowski
July 17, 2015

Broad Technology labs provides sequencing data in a directory structure like
this:

    C1-123_2012-06-01_2012-06-03
    ├── 1
    │   ├── HCHT1BGXX.1.AGGCAGAA_AGAGGATA.unmapped.1.fastq.gz
    │   ├── HCHT1BGXX.1.AGGCAGAA_AGAGGATA.unmapped.2.fastq.gz
    │   ...
    ├── 2
    │   ├── HCHT1BGXX.2.AGGCAGAA_AGAGGATA.unmapped.1.fastq.gz
    │   ├── HCHT1BGXX.2.AGGCAGAA_AGAGGATA.unmapped.2.fastq.gz
    │   ...
    ...
    │
    └── info
        ├── logs
        │   ├── generateGetManifest.HCHT1BGXX.0.0.log
        │   ├── generateGetSite.HCHT1BGXX.0.0.log
        │   ├── ID_riker-12345-1234567890123.json
        │   ├── logs.tar.gz
        │   ├── sendFileEmail.sendGetSiteEmail.HCHT1BGXX.0.0.log
        │   └── workflow.log
        └── summary

This script reads the JSON file:

    info/logs/ID_riker-12345-1234567890123.json
    
and prints the Unix commands to merge FASTQ files from multiple lanes:

    gzip -cd 1/HCHT1BGXX.1.AGGCAGAA_AGAGGATA.unmapped.1.fastq.gz \
        2/HCHT1BGXX.2.AGGCAGAA_AGAGGATA.unmapped.1.fastq.gz \
        | pigz > sampleAlias.R1.fastq.gz

If we execute the commands, we will create new files like this:

    C1-166_2015-07-02_2015-07-06
    ├── sampleAlias.R1.fastq.gz
    └── sampleAlias.R2.fastq.gz

LICENSE

This is free and unencumbered software released into the public domain.
Anyone is free to copy, modify, publish, use, compile, sell, or
distribute this software, either in source code form or as a compiled
binary, for any purpose, commercial or non-commercial, and by any
means.

In jurisdictions that recognize copyright laws, the author or authors
of this software dedicate any and all copyright interest in the
software to the public domain. We make this dedication for the benefit
of the public at large and to the detriment of our heirs and
successors. We intend this dedication to be an overt act of
relinquishment in perpetuity of all present and future rights to this
software under copyright law.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
IN NO EVENT SHALL THE AUTHORS BE LIABLE FOR ANY CLAIM, DAMAGES OR
OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
OTHER DEALINGS IN THE SOFTWARE.

For more information, please refer to <http://unlicense.org/>
"""

import json
import os
import argparse

# We want to ignore this error:
#   IOError: [Errno 32] Broken pipe
from signal import signal, SIGPIPE, SIG_DFL
signal(SIGPIPE,SIG_DFL)

def main():
    args = get_args()

    x = json.loads(args.json.read())

    sampleAliases = get_sampleAliases(x)

    for sampleAlias in sampleAliases:

        for end in (1, 2):

            fastqs = filenames(x, sampleAlias, end)

            outform = '{sampleAlias}.R{end}.fastq.gz'
            
            d = {
                'sampleAlias': sampleAlias,
                'end': end
            }

            out = outform.format(**d)

            cmdform = 'gzip -cd {} | pigz > {}'

            print cmdform.format(' '.join(fastqs), out)


def get_args():
    parser = argparse.ArgumentParser(
        description="""Print commands needed to merge FASTQ files from
        multiple lanes."""
    )
    parser.add_argument(
        'json', metavar='FILE', type=argparse.FileType('r'),
        help='JSON file found in info/logs/*.json'
    )
    return parser.parse_args()


def filenames(js, sampleAlias, end = 1):
    """Returns a list of filenames corresponding to a sampleAlias.
    """
    fname = '{lane}/{flowcellBarcode}.{lane}.{barcode1}_{barcode2}.unmapped.{end}.fastq.gz'

    flowcellBarcode = js['workflow']['flowcellBarcode']

    lanes = js['workflow']['lanes']

    retval = []

    for lane_i, lane in enumerate(lanes, 1):
        libraries = lane['libraries']

        library_i = 0
        for i, x in enumerate(libraries):
            if x['sampleAlias'] == sampleAlias:
                library_i = i

        library = libraries[library_i]

        barcode1, barcode2 = library['molecularBarcodeSequences']

        d = {
            'flowcellBarcode': flowcellBarcode,
            'lane': lane_i,
            'barcode1': barcode1,
            'barcode2': barcode2,
            'end': end
        }

        filename = fname.format(**d)

        assert os.path.isfile(filename)

        retval.append(fname.format(**d))

    return retval


def get_sampleAliases(js):
    """Returns a list of sampleAliases.
    """
    retval = []
    for lane in js['workflow']['lanes']:
        for library in lane['libraries']:
            sampleAlias = library['sampleAlias']
            if not sampleAlias in retval:
                retval.append(sampleAlias)
    return retval


if __name__ == '__main__':
    main()