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Revision 1.5 - (download) (as text) (annotate)
Tue May 20 16:57:20 2008 UTC (11 years, 6 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, 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, 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
Changes since 1.4: +1 -1 lines
SeqStat lib fix

use Data::Dumper;
use Carp;
use FIG_Config;

use lib '/vol/cee-2007-1108/linux-debian-x86_64/lib/perl5/site_perl/5.8.8/Bio/Tools';
use SeqStats;
use pICalculator;
use FIGV;

my $jobdir = shift(@ARGV);
my $genome = shift(@ARGV);
my $date = localtime();

if(! -d "$jobdir/rp/$genome/attributes"){
    `mkdir $jobdir/rp/$genome/attributes`;
}

my $fig = new FIGV("$jobdir/rp/$genome");

open(MW,">$jobdir/rp/$genome/attributes/molecular_weight_for_$genome.txt");
open(ISO,">$jobdir/rp/$genome/attributes/isoelectric_point_for_$genome.txt");

print MW "$genome\tmolecular_weight_computed_against_all_pegs\t$date\n";
print ISO "$genome\tisoelectric_point_computed_against_all_pegs\t$date\n";

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";
}

close(ISO);
close(MW);	

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