Assuming your shell is bash....
With this exported function
function slice {
# PURPOSE: After an optional -h lines of header
(which are echoed
# unless supressed with <-sh>), echo every <-n>th
line (default:
# every 1 line) starting with the <-m>th (counting
from 1, starting
# with the first line after the header, default:
starting with the
# <n-1>th line.)
# AUTHOR: malcolm_cook@stowers.org
# EXAMPLE: slice -h=1 -sh -n=5 foo.tab > foo_every_fifth_line_after_the_one_line_header.tab
# set -e ;
perl -snwe 'BEGIN{our $n||=1; our $m=($n) unless
defined($m); $m-=1; our $h||=0; die "required: m < n" unless $m < $n; our $sh} print $_ if (($. > $h ) ? (($. -1 - $h) % $n == $m) : ! $sh)' -- $@
}
export -f slice
...you can create a parallel jobs where each job
greps a slice of in.bam
You would pass parallels {#} as the value for
–m and the same value you pass as –j to parallel as the value for –n
You’ll probably need to use parallels –q and have
each job call bash.
The following is untested.
parallel –j 10 –q ‘bash –c “samtools view in.bam | slice –n=10 –m={#} | bash –c fgrep -w -f read.ids”’ > alignments.txt
The output will have the slices interwoven.
From:
parallel-bounces+mec=stowers.org@gnu.org [mailto:parallel-bounces+mec=stowers.org@gnu.org]
On Behalf Of Nathan S. Watson-Haigh
Sent: Friday, August 09, 2013 12:54 AM
To: parallel@gnu.org
Subject: Parallelising grep
I have a SAM/BAM file and I’d like to grep for alignments of certain reads IDs. I have the read ID strings in another file. I’m currently
doing this with:
$ samtools view in.bam | fgrep -w -f read.ids > alignments.txt
Is it possible to parallelise the grep by having each grep process a different subset of read iDs from the read.ids file? Or is there an alternative
way to parallelise this which I have overlooked?
Cheers,
Nathan
--
Nathan S. Watson-Haigh, PhD
Research Fellow in Bioinformatics
Australian Centre for Plant Functional Genomics (ACPFG)
School of Agriculture, Food and Wine
University of Adelaide Waite Campus
Plant Genomics Centre
Hartley Grove, Urrbrae
SA 5064
Phone: +61
8 8313 2046
Mobile: +61 438 711 615
Skype:
nathanhaigh
Email:
nathan.haigh@acpfg.com.au
Web:
http://www.acpfg.com.au/bioinformatics
LinkedIn
http://www.linkedin.com/profile/view?id=114191748
Github:
https://github.com/nathanhaigh/
https://gist.github.com/nathanhaigh/
Twitter:
@watsonhaigh
RID:
B-9833-2008
ResearchGate:
Nathan_Watson-Haigh
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