coela

use 5.12.2;
use JSON;
use Data::Dumper;
use LWP::Simple;
my @json_places = (
    ['Complete' , "http://www.genomesonline.org/complete_published.json"],
    ['Bacteria Ongoing' , "http://www.genomesonline.org/bacterial_ongoing.json"],
    ['Eukaryal Ongoing' , "http://www.genomesonline.org/eukaryal_ongoing.json"],
    ['Archaeal Ongoing' , "http://www.genomesonline.org/archaeal_ongoing.json"],
    ['Metagenome' , "http://www.genomesonline.org/microbial.json"],

coela

use G;
use 5.12.4;

my $gb = load('ecoli');
$gb->{$_}->{product} = '' for $gb->cds();
for ($gb->cds()){
  my $l = length $gb->{$_}->{translation};
  $gb->{$_}->{product} = 'ribosomal fucking protein' if $l >=500;
}
say Dumper w_value ($gb);

coela

sub add_free_energy{
  my $gb = shift;
  for my $cds ($gb->feature('CDS')){
    my $before = $gb->before_startcodon($cds,4);
    my $after = substr ($gb->get_geneseq($cds), 0 , 30);
    my $freeenergy = `echo "$after" | hybrid-ss-min --stream`;
    chomp $freeenergy;
    $gb->{$cds}->{'free_energy'} = $freeenergy;
  }
  return $gb;

coela

use Furl;

my $furl = Furl->new(
    agent   => 'MyGreatUA/2.0',
    timeout => 10,
    );

my %query = (
    u => 'ebisama',
    );

coela

use 5.14.2;
use Data::Dumper;

my @array;

for (1..100) {
  my $gene;
  $gene->{tpi} = $_; 
  $gene->{start} = $_ * 100;
  push @array,$gene;

coela

use strict;
print "hoge";

coela

use 5.14.2;
use warnings;
use Data::Dumper;
use SWISS::Entry;
use SWISS::IDs;
use JSON;
use GraphViz;
use GO::Parser;

use lib qw{../lib};

coela

#!/usr/bin/env perl
use strict;
use warnings;
use Data::Dumper;
use G;

my $eco = new G( "ecoli", "no msg" );
my @cds;

for my $cds ($eco->cds()) {

coela

use strict;
use G;
use Data::Dumper;

my $gb = new G ("ecoli", "no msg");
open my $FILE, $ARGV[0] || die;

my $bunkatu = int (length ($gb->{SEQ}) /20);
cai($gb);
my @feature;

coela

#!/usr/bin/perl

use strict;
use warnings;
use LWP::UserAgent;
use HTTP::Request::Common qw(POST);

my $referer = 'http://www.phosphosite.org/sequenceLogoAction.do';
my $url = 'http://www.phosphosite.org/sequenceLogoSubmitAction.do';