Raj at 05:21, 28 October 2016

2016-10-28T05:21:55Z

← Older revision		Revision as of 05:21, 28 October 2016
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			[[Category:Bioinformatics]]

	<source lang=perl>		<source lang=perl>
	#! /usr/bin/perl -w		#! /usr/bin/perl -w

Raj at 18:08, 28 December 2009

2009-12-28T18:08:06Z

← Older revision		Revision as of 18:08, 28 December 2009
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	$sequence = $seq->seq;		$sequence = $seq->seq;

			# trimming part
			$identifier =~ s/(scaffold_[0-9]+):.+/$1/g;
	$sequence =~ s/(.+)/\U$1/g;		$sequence =~ s/(.+)/\U$1/g;

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

2009-12-28T17:24:15Z

New page: <source lang=perl> #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Parses a multi fasta # -> Makes ...

New page

<source lang=perl>
#! /usr/bin/perl -w
# *************************************************************
# This Programme does the following in sequence
# -> Parses a multi fasta
# -> Makes the small letters on CAPS
# -> Write 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 $datadir = "$path/euca/data/grandis/scaffold/dl";
my $resdir = "$path/euca/data/grandis/scaffold/trim";
my ($i, $file)= $_;
my (@files)= @_;

# At the top: Time Start
my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);

# Start your Hack!

# Get ready with the folders
if (-e "$resdir") {`rm -fr $resdir`;}
if (! -e "$resdir") {`mkdir $resdir`;}

opendir (DIR, "$datadir") or die $!;
@files = readdir(DIR);
close(DIR);

#Lets Grab the number of files
my $count_files = @files;
$i = 0;

foreach my $file(@files) {
next if ($file !~ m/.txt/g);

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

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

$sequence =~ s/(.+)/\U$1/g;

my $fasta = ">$identifier\n$sequence\n";

open (FH, ">>".$resdir."/".$file);
print FH "$fasta";
close FH;

print "\r\tWritten $file . Writing $i of $count_files files"

}
}

print "\nAll Done!\n\n";

# At the End: Time Calculation
my ($sec_,$min_,$hour_,$mday_,$mon_,$year_,$wday_,$yday_,$isdst_) = localtime(time);
my $days = $mday_-$mday;
my $hours = $hour_-$hour;
my $mins = $min_-$min;
my $secs = $sec_-$sec;
print "\n------------------------\nDuration: ";
if ($days>0) { print "$days days";}
if ($hours>0) { print ": $hours hours";}
if ($mins>0) { print ": $mins mins";}
if ($secs>0) { print ": $secs secs";}
print "\n------------------------\n";

# END
</source>

Caps fasta.pl - Revision history

Raj at 05:21, 28 October 2016

Raj at 18:08, 28 December 2009

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