Trim fasta.pl - Revision history

Raj at 11:29, 20 May 2016

2016-05-20T11:29:29Z

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Raj at 09:55, 23 April 2011

2011-04-23T09:55:09Z

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Raj at 18:41, 2 January 2010

2010-01-02T18:41:55Z

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Raj at 11:29, 26 December 2009

2009-12-26T11:29:36Z

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Raj at 15:25, 25 December 2009

2009-12-25T15:25:39Z

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Raj: New page:

 #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Parses a multi fasta # -> Removes the sequenc...

2009-12-25T14:30:43Z

New page: <pre> #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Parses a multi fasta # -> Removes the sequenc...

New page

<pre>
#! /usr/bin/perl -w
# *************************************************************
# This Programme does the following in sequence
# -> Parses a multi fasta
# -> Removes the sequence if they have <50bp and of 'N'
# -> Capture the results

# Author : Rajkumar (itc@rajkumar.in)
# Release: DEC 2009
# *************************************************************

# Libraries
use strict;
use Bio::Perl;
use Bio::SeqIO;

# Variables
my $path = "/home/raj/bio";
my $multifasta = "$path/euca/data/globulus/globulus_est.fa";

# making several Fasta files of GDNA

my $in = Bio::SeqIO->new(-file => "$multifasta", -format => 'Fasta');
my $identifier;
my $sequence;

while ( my $seq = $in->next_seq() ) {
$identifier = $seq->id;
$sequence = $seq->seq;

my ($fasta) = $_;
$fasta = ">$identifier\n$sequence\n";

my $count_seq = length($sequence);
my $count_N = ($sequence =~ tr/N//);
my $math = $count_seq * 0.2;

$sequence =~ s/-/N/;
if ($count_seq < 50){ next; }
if ($count_N > $math){ next; }

print $identifier."\n";

}

# END
</pre>