Raj at 18:49, 3 January 2010

2010-01-03T18:49:10Z

← Older revision		Revision as of 18:49, 3 January 2010
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	#END		#END
	</source>		</source>
			[[Category:Bioinformatics]]

Raj at 18:03, 1 January 2010

2010-01-01T18:03:52Z

← Older revision		Revision as of 18:03, 1 January 2010
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	* Fetching Fasta as separate components		* Fetching Fasta as separate components
	<~~pre~~>		<source lang=perl>
	#!/usr/bin/perl -w		#!/usr/bin/perl -w

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	`rm tempfile`;		`rm tempfile`;
	#END		#END
	</~~pre~~>		</source>

Raj: New page: * Fetching Fasta as separate components

 #!/usr/bin/perl -w  #---------------------------- # Description # Remmoves the new line if exists in multifasta ignoring the sequence identifi...

2008-10-21T19:51:40Z

New page: * Fetching Fasta as separate components <pre> #!/usr/bin/perl -w #---------------------------- # Description # Remmoves the new line if exists in multifasta ignoring the sequence identifi...

New page

* Fetching Fasta as separate components
<pre>
#!/usr/bin/perl -w

#----------------------------
# Description
# Remmoves the new line if exists in multifasta ignoring the sequence identifier
# Usage: Type infilename and Capture the output
#--------------------------------

# Use of functions
use strict;
use Bio::SeqIO;

# Variables
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/Note //g;
$input =~ s/[ ]+/_/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";
}
`rm tempfile`;
#END
</pre>

Fetching Fasta - Revision history

Raj at 18:49, 3 January 2010

Raj at 18:03, 1 January 2010

Raj: New page: * Fetching Fasta as separate components
#!/usr/bin/perl -w #---------------------------- # Description # Remmoves the new line if exists in multifasta ignoring the sequence identifi...