hoge.pl

hoge.pl

#!/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()) {
  for ($eco->{$cds}->{start} .. $eco->{$cds}->{end}) {
    $cds[$_] = $cds;
  }
}

my @cds_dir;
my @cds_compl;

foreach my $cds ( $eco->cds() ){
  if ( $eco->{$cds}->{direction} eq "direct" ) {
    push @cds_dir, $cds;
  }
  else {
    push @cds_compl, $cds;
  }
}

print "gene\t", "count\t", "product\t", "function\n";

my $hogehoge1;
my $hogehoge2;
my $cds_count = 0;
my $sd_count = 0;

my %direct_pos_to_oligomers = oligomer_search($eco->{SEQ}, "ggnggn", -return=>"both");
foreach my $pos_d ( sort{$a <=> $b} keys %direct_pos_to_oligomers ) { 
  my $feature = $cds[$pos_d]; 
  if ( $feature ) { 
    $sd_count++;
    my $gene = $eco->{$feature}->{gene}; 
    $hogehoge1->{$gene}->{gene_in} = $eco->{$feature}->{gene};
    $hogehoge1->{$gene}->{sd_count_in} = $sd_count; 
    $hogehoge1->{$gene}->{product_in} = $eco->{$feature}->{product};
    $hogehoge1->{$gene}->{function_in} = $eco->{$feature}->{function};
  }
}

my $cds_count_compl = 0;
my $cds_count_compl2 = 0;

my %compl_pos_to_oligomers = oligomer_search($eco->{SEQ}, "nccncc", -return=>"both");
foreach my $pos_c ( sort{$a <=> $b} keys %compl_pos_to_oligomers ) {
my $feature3 = $cds[$pos_c];
if ( $feature3 ) {
$sd_count++;
my $gene = $eco->{$feature3}->{gene};
$hogehoge1->{$gene}->{gene_in} = $eco->{$feature3}->{gene};
$hogehoge1->{$gene}->{sd_count_in} = $sd_count; 
$hogehoge1->{$gene}->{product_in} = $eco->{$feature3}->{product};
$hogehoge1->{$gene}->{function_in} = $eco->{$feature3}->{function};
}
}

for my $gene ( keys %$hogehoge1 ) {
print join "\t", ($hogehoge1->{$gene}->{gene_in},$hogehoge1->{$gene}->{sd_count_in},$hogehoge1->{$gene}->{product_in},$hogehoge1->{$gene}->{function_in});
print "\n";
}