This script takes the name of the file and the number of sequences you want and outputs that number of randomly selected sequences.
It is simple, fast and should handle any size of input file with minimal memory usage:
#! perl -slw
use strict;
use List::Util qw[ shuffle ];
$/ = '>';
open FASTA, '<:raw', $ARGV[0] or die $!;
my @seqPosns;
push @seqPosns, tell( FASTA ) while <FASTA>;
@seqPosns = shuffle @seqPosns;
for ( @seqPosns[ 0 .. $ARGV[ 1 ] // 10 ] ) {
seek FASTA, $_, 0;
my $seq = <FASTA>;
chomp( $seq ); chop( $seq );
print '>', $seq;
}
close FASTA;
__END__
C:\test>988096.pl C:/dell/test/LCS/bioMan.fasta 2
>af418682
TTCCACAACTTTCCACCAAGCTCTACAAGATCCCAGAGTCAGGGGCCTGTATTTTCC
TGGGTCTTTTGGGCTTTGCCGCTCCATTTACACAATGTGGTTATCCTGCATTAATGC
ACTTCTTTCCTTCAGTACGAGATCTCCTAGATACCGCCTCAGCTCTATATCGGGAAG
TCAAACAATCCAGATTGGGACTTCAACCCCATCAAGGACCACTGGCCACAAGCCAAC
>ab033557
CTCCACGACATTCCACCAAGCTCTGCTAGATCCCAGAGTGAGGGGCCTTTACTTTCC
TGGGTCTTTTGGGCTTTGCTGCCCCTTTTACACAATGTGGCTATCCTGCCTTAATGC
ACTTCTTTCCTTCCATTCGAGATCTTCTCGACACCGCCTCTGCTCTGTATCGGGAGG
TCAAACAATCCAGATTGGGACTTCAACCCCAACAAGGATCAATGGCCAGAAGCAAAT
>x97850
CTCCACAACTTTCCTCCAAACTCTTCAAGATTCCAGAGTCAGGGCCCTGTACCTTCC
TGGGTCTTTTGGGGTTTGCCGCCCCTTTCACGCAATGTGGATATCCTGCTTTAATGC
ACTTTTTTCCTTCTATTCGAGATCTCCTCGACACCGCCTCTGCTCTGTATCGGGAGG
TCAGAAAATCCAGATTGGGACCTCAACCCGCACAAGGACAACTGGCCGGACGCCAAC
With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday'
Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
"Science is about questioning the status quo. Questioning authority".
-
Are you posting in the right place? Check out Where do I post X? to know for sure.
-
Posts may use any of the Perl Monks Approved HTML tags. Currently these include the following:
<code> <a> <b> <big>
<blockquote> <br /> <dd>
<dl> <dt> <em> <font>
<h1> <h2> <h3> <h4>
<h5> <h6> <hr /> <i>
<li> <nbsp> <ol> <p>
<small> <strike> <strong>
<sub> <sup> <table>
<td> <th> <tr> <tt>
<u> <ul>
-
Snippets of code should be wrapped in
<code> tags not
<pre> tags. In fact, <pre>
tags should generally be avoided. If they must
be used, extreme care should be
taken to ensure that their contents do not
have long lines (<70 chars), in order to prevent
horizontal scrolling (and possible janitor
intervention).
-
Want more info? How to link
or How to display code and escape characters
are good places to start.
|