[Bio] / FigKernelScripts / compute_mw_and_pi_with_BioPerl.pl Repository:
ViewVC logotype

View of /FigKernelScripts/compute_mw_and_pi_with_BioPerl.pl

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.1 - (download) (as text) (annotate)
Wed Jul 25 18:11:41 2007 UTC (12 years, 3 months ago) by mkubal
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, rast_rel_2008_06_18, myrast_rel40, rast_rel_2008_06_16, mgrast_dev_05262011, rast_rel_2008_12_18, mgrast_dev_04082011, rast_rel_2008_07_21, rast_rel_2010_0928, rast_2008_0924, mgrast_version_3_2, mgrast_dev_12152011, rast_rel_2008_04_23, mgrast_dev_06072011, rast_rel_2008_09_30, rast_rel_2009_0925, rast_rel_2010_0526, rast_rel_2014_0729, mgrast_dev_02212011, rast_rel_2010_1206, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2010_0118, mgrast_rel_2008_0924, mgrast_rel_2008_1110_v2, rast_rel_2009_02_05, rast_rel_2011_0119, mgrast_rel_2008_0625, mgrast_release_3_0_4, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_1, mgrast_dev_03312011, mgrast_release_3_1_2, mgrast_release_3_1_1, mgrast_release_3_1_0, mgrast_dev_04132011, rast_rel_2008_10_09, mgrast_dev_04012011, rast_release_2008_09_29, mgrast_rel_2008_0806, mgrast_rel_2008_0923, mgrast_rel_2008_0919, rast_rel_2009_07_09, rast_rel_2010_0827, mgrast_rel_2008_1110, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, mgrast_rel_2008_0917, rast_rel_2008_10_29, mgrast_dev_04052011, mgrast_dev_02222011, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
computes mw and pi for all pegs in complete genomes

#!/usr/bin/env /home/mkubal/public_html/FIGdisk/env/cee/bin/perl

BEGIN {
    @INC = qw(
              /home/mkubal/public_html/FIGdisk/dist/releases/dev/cee/lib
              /home/mkubal/public_html/FIGdisk/dist/releases/dev/cee/lib/PPO
              /home/mkubal/public_html/FIGdisk/dist/releases/dev/cee/lib/FigKernelPackages
              /home/mkubal/public_html/FIGdisk/dist/releases/dev/cee/lib/WebApplication
              /home/mkubal/public_html/FIGdisk/dist/releases/dev/cee/lib/FortyEight
              /home/mkubal/public_html/FIGdisk/dist/releases/dev/cee/lib/SeedViewer
              /home/mkubal/public_html/FIGdisk/dist/releases/dev/cee/lib/Flower
              /home/mkubal/public_html/FIGdisk/dist/dev/cee/lib
              /home/mkubal/public_html/FIGdisk/dist/dev/cee/lib/FigKernelPackages
              /home/mkubal/public_html/FIGdisk/env/cee/lib/perl5/5.8.7/i686-linux
              /home/mkubal/public_html/FIGdisk/env/cee/lib/perl5/5.8.7
              /home/mkubal/public_html/FIGdisk/env/cee/lib/perl5/site_perl/5.8.7/i686-linux
              /home/mkubal/public_html/FIGdisk/env/cee/lib/perl5/site_perl/5.8.7
              /home/mkubal/public_html/FIGdisk/env/cee/lib/perl5/site_perl
	      /home/mkubal/public_html/FIGdisk/env/cee/lib/perl5/site_perl/5.8.7/Bio/Tools
              .
              /home/mkubal/public_html/FIGdisk/config

	      );
}

use Data::Dumper;
use Carp;
use FIG_Config;
$ENV{'BLASTMAT'} = "/home/mkubal/public_html/FIGdisk/BLASTMAT";
$ENV{'FIG_HOME'} = "/home/mkubal/public_html/FIGdisk";

use SeqStats;
use pICalculator;
use FIG;

open(MW,">/vol/seed-attributes/molecular_weight/molecular_weight.txt");
open(ISO,">/vol/seed-attributes/isoelectric_point/isoelectric_point.txt");

$fig = new FIG;

my @genomes = $fig->genomes('complete');
foreach my $genome (@genomes){
    my @pegs = $fig->pegs_of($genome);
    foreach $peg (@pegs){
	my $seq = $fig->get_translation($peg);
	$mw_seqobj = Bio::PrimarySeq->new(-seq=>$seq,
					  -alphabet=>'protein',
					  -id=>'test');
	
	$weight = Bio::Tools::SeqStats->get_mol_wt($mw_seqobj);
	print MW "$peg\tmolecular_weight\t$$weight[0]\n";
	#print "$peg\tmolecular_weight\t$$weight[0]\n";
	
	$pi_seqobj = Bio::Seq->new(-seq=>$seq,
				   -alphabet=>'protein',
				   -id=>'test');
	
	$calc = Bio::Tools::pICalculator->new(-places => 2);
	$calc->seq($pi_seqobj);
	$iep = $calc->iep;
	print ISO "$peg\tisoelectric_point\t$iep\n";
	#print "$peg\tisoelectric_point\t$iep\n";
    }
}
	

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3