Display full taxon path from NCBI GI number - perl

Question

I prepared the following script that takes a GI ID number from NCBI that I prepared in my tsv file and prints the scientific name associated with the ID:
#!/usr/bin/perl
use strict;
use warnings;
use Bio::DB::Taxonomy;
my ($filename) = #ARGV;
open my $fh, '<', $filename or die qq{Unable to open "$filename": $!};
while(<>) {
my ($taxonid, $counts) = (split /\t/);
for my $each($taxonid) {
print "$each\n";
my $db = Bio::DB::Taxonomy->new(-source => 'entrez');
my $taxon = $db->get_taxon(-taxonid => $taxonid);
print "Taxon ID is $taxon->id, \n";
print "Scientific name is ", $taxon->scientific_name, "\n";
}
}
With this script, I receive the following:
1760
Taxon ID is Bio::Taxon=HASH(0x33a91f8)->id,
Scientific name is Actinobacteria
What I want to do
Now the next step is for me to list the full taxon path of the bacteria in question. So for the above example, I want to see k__Bacteria; p__ Actinobacteria; c__ Actinobacteria as output. Furthermore, I want the GI IDs on my table to be repliaced with this full taxon path.
In which direction should I go?

Answer 1

First, I notice you open $filename which is your first command line argument, but you don't use the file pointer $fh you created.
So, these two lines are not needed in your case because you already do the trick with <>
my ($filename) = #ARGV;
open my $fh, '<', $filename or die qq{Unable to open "$filename": $!};
Next. I don't know what is inside your filename and your database so I cannot help you more. Can you provide an example of what is inside your database and your file?
One more thing, what I can see here is that you may not need to create your $db instance inside the loop.
#!/usr/bin/perl
use strict;
use warnings;
use Bio::DB::Taxonomy;
my $db = Bio::DB::Taxonomy->new(-source => 'entrez');
while(<>) {
my ($taxonid, $counts) = (split /\t/);
for my $each($taxonid) {
print "$each\n";
my $taxon = $db->get_taxon(-taxonid => $taxonid);
print "Taxon ID is $taxon->id, \n";
print "Scientific name is ", $taxon->scientific_name, "\n";
}
}
Edit
From your command Is is hard to help you. When you write
my $taxon = $db->get_taxon(-taxonid => $taxonid);
You receive a Bio::Taxon node where the documentation ca be found here
I don't know what k__Bacteria; p__ Actinobacteria; c__ Actinobacteria representy for you. Is it an information offered by a Bio::Taxon node?
Anyway, you can still explore $taxon with this:
#!/usr/bin/env perl
# Author: Yves Chevallier
# Date:
use strict;
use warnings;
use Data::Dumper;
use Bio::DB::Taxonomy;
my $db = Bio::DB::Taxonomy->new(-source => 'entrez');
while(<DATA>) {
my ($taxonid, $counts) = (split /\t/);
for my $each($taxonid) {
print "$each\n";
my $taxon = $db->get_taxon(-taxonid => $taxonid);
print Dumper $taxon;
print "Taxon ID is $taxon->id, \n";
print "Scientific name is ", $taxon->scientific_name, "\n";
}
}
__DATA__
12 1760