Raj at 18:48, 3 January 2010

2010-01-03T18:48:55Z

← Older revision		Revision as of 18:48, 3 January 2010
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	</source>		</source>
			[[Category:Bioinformatics]]

Raj at 04:32, 27 December 2009

2009-12-27T04:32:59Z

← Older revision		Revision as of 04:32, 27 December 2009
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	<~~pre~~>		<source lang=perl>

	#! /usr/bin/perl -w		#! /usr/bin/perl -w
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	# END		# END

	</~~pre~~>		</source>

Raj: New page:

  #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Open a multi fasta file # -> Count the numbe...

2009-10-25T13:10:24Z

New page: <pre> #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Open a multi fasta file # -> Count the numbe...

New page

<pre>

#! /usr/bin/perl -w
# *************************************************************
# This Programme does the following in sequence
# -> Open a multi fasta file
# -> Count the number of bases in each fasta
# -> output need to be captured
# Author: Rajkumar (itc@rajkumar.in)

# *************************************************************

# Libraries
use strict;
use Bio::SeqIO;

# Variables
my $path = "/home/raj/bio";

# Getting the input file
my $argcount = @ARGV;
if ($argcount !=1 ) {die "\n\t ->Usage: Type infile!\n\n";}
my ($infile,$outfile) = @ARGV;
my @seq;

# Function
chomp($infile);
my $input = `cat $infile`;

$input =~ s/[\"|(|)|:]//g;
$input =~ s/[ ]+/_/g;
$input =~ s/.abi//g;

open(TEMP, ">tempfile");
print TEMP $input;
close TEMP;

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

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

# print ">$identifier\n$sequence\n";

my $length = ($sequence =~ tr/[A-Z]|[a-z]//);
print "$identifier\t$length\n";

}
`rm tempfile`;

# END

</pre>

Count fasta characters - Revision history

Raj at 18:48, 3 January 2010

Raj at 04:32, 27 December 2009

Raj: New page:
#! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Open a multi fasta file # -> Count the numbe...