EntrezGeneID get sequence

entrenzgeneid

#!/usr/bin/perl
use strict;
use warnings;
use Bio::DB::EUtilities;
 
# this needs to be a list of EntrezGene unique IDs
my @ids   = @ARGV;
 
my $eutil   = Bio::DB::EUtilities->new(-eutil => 'esearch',
                                       -email => 'mymail@foo.bar',
                                       -db    => 'gene',
                                       -term  => join(',',@ids));

my @gene_ids = $eutil->get_ids;

$eutil   = Bio::DB::EUtilities->new(-eutil => 'esummary',
                                       -email => 'mymail@foo.bar',
                                       -db    => 'gene',
                                       -id    => \@gene_ids);
 
my $fetcher = Bio::DB::EUtilities->new(-eutil   => 'efetch',
                                       -email => 'mymail@foo.bar',
                                       -db      => 'nucleotide',
                                       -rettype => 'gb');
 
while (my $docsum = $eutil->next_DocSum) {
    # to ensure we grab the right ChrStart information, we grab the Item above
    # it in the Item hierarchy (visible via print_all from the eutil instance)
    my ($item) = $docsum->get_Items_by_name('GenomicInfoType');
 
    my %item_data = map {$_ => 0} qw(ChrAccVer ChrStart ChrStop);
 
    while (my $sub_item = $item->next_subItem) {
        if (exists $item_data{$sub_item->get_name}) {
            $item_data{$sub_item->get_name} = $sub_item->get_content;
        }
    }
    # check to make sure everything is set
    for my $check (qw(ChrAccVer ChrStart ChrStop)) {
        die "$check not set" unless $item_data{$check};
    }
 
    my $strand = $item_data{ChrStart} > $item_data{ChrStop} ? 2 : 1;
    printf("Retrieving %s, from %d-%d, strand %d\n", $item_data{ChrAccVer},
                                                    $item_data{ChrStart},
                                                    $item_data{ChrStop},
                                                    $strand
                                                    );
 
    $fetcher->set_parameters(-id => $item_data{ChrAccVer},
                             -seq_start => $item_data{ChrStart} -5000 ,
                             -seq_stop  => $item_data{ChrStop} + 5000 ,
                             -strand    => $strand);
    print $fetcher->get_Response->content;
}

gistfile1.txt

#!/usr/bin/perl
use strict;
use warnings;
use Bio::DB::EUtilities;
 
# this needs to be a list of EntrezGene unique IDs
my @ids   = @ARGV;
 
my $eutil   = Bio::DB::EUtilities->new(-eutil => 'esearch',
                                       -email => 'mymail@foo.bar',
                                       -db    => 'gene',
                                       -term  => join(',',@ids));

print join(",",$eutil->get_ids);