Raj at 13:44, 28 December 2009

2009-12-28T13:44:47Z

@@ Line 18: / Line 18: @@
 ## Variables
-	my $path     = "/home/raj/bio";
+	my $path         = "/home/raj/bio";
-	my $resdir   = "$path/euca/unigene";
+	my $resdir       = "$path/euca/unigene";
-	my $singlets = "$resdir/globulus_singlets.fa";
+	my $singlets     = "$resdir/globulus_singlets.fa";
-	my $contigs  = "$resdir/globulus_contigs.fa";
+	my $contigs      = "$resdir/globulus_contigs.fa";
-	my $unigenes = "$resdir/globulus_unigenes.fa";
+	my $unigenes     = "$resdir/globulus_unigenes.fa";
@@ Line 32: / Line 33: @@
 	if (-e "$contigs") {`rm  $contigs`;}
 	if (-e "$unigenes") {`rm  $unigenes`;}
 	foreach my $asm (@asmdir) {
-		`cat $resdir/result/$asm/contigs >>$contigs`;
+		`cat $resdir/result/$asm/contigs >>$contigs_temp`;
 		`cat $resdir/result/$asm/singlets >>$singlets`;
+	}
 	`cat $contigs $singlets >$unigenes`;
 # END
 </source>

Raj: New page: #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Open a results folder of TGICL...

2009-12-26T15:13:54Z

New page: <source lang=perl> #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Open a results folder of TGICL...

New page

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

# *************************************************************
# This Programme does the following in sequence
# -> Open a results folder of TGICL
# -> parse the contigs and singlets
# -> Output as multifasta of single file
# Author: Rajkumar (itc@rajkumar.in)

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

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

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

my $singlets = "$resdir/globulus_singlets.fa";
my $contigs = "$resdir/globulus_contigs.fa";
my $unigenes = "$resdir/globulus_unigenes.fa";

my @asmdir = ("asm_1", "asm_2", "asm_3", "asm_4");

# Getting the grip
if (-e "$singlets") {`rm $singlets`;}
if (-e "$contigs") {`rm $contigs`;}
if (-e "$unigenes") {`rm $unigenes`;}

foreach my $asm (@asmdir) {
`cat $resdir/result/$asm/contigs >>$contigs`;
`cat $resdir/result/$asm/singlets >>$singlets`;
}
`cat $contigs $singlets >$unigenes`;

# END
</source>

Tgicl parse.pl - Revision history

Raj at 13:44, 28 December 2009

Raj: New page: #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Open a results folder of TGICL...