Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-09-05

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All times shown according to UTC.

Time Nick Message
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14:09 paul15024 hi, anybody on?
14:25 Jun yes?
14:49 paul15024 jun, do you know how to get a taxonid from an accession number?
14:50 paul15024 i'm trying to categorize blast output by taxonomy
14:50 paul15024 i have an accession number and want to find an efficient way to get the taxonomy information associated with that accession number
14:51 paul15024 i usually resort to downloading each genbank record and then parsing the ORGANISM field to get the taxonomy info
14:51 paul15024 but this becomes inefficient when i have alot of accession numbers
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15:17 Jun Ok, paul15024, You can read this HOWTO on Bio::EUtilities
15:18 Jun http://www.bioperl.org/wiki​/HOWTO:EUtilities_Cookbook
15:19 Jun You can use Bio::EUtilities to retrieve taxonomy information in batch mode
15:22 paul15024 jun, thanks for the link
15:23 paul15024 i've perused it but didn't see any clear example of how to go from an accession number to taxonomy information
15:24 paul15024 i'm going to look at the Bio::EUtilities documentation now
15:27 paul15024 unfortunately, the word 'accession' nor 'taxonomy' appears in Bio::DB::EUtilites documentation
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15:33 paul15024 using eutils seems confusing
15:34 paul15024 can anybody provide some direct help in how to go from an accession number to the classification array in the genbank record (field is 'ORGANISM')?
15:35 paul15024 for example, if the accession number is J02400, I want the output to be 'Viruses; dsDNA viruses, no RNA stage; Polyomaviridae; Polyomavirus; Simian virus 40'
15:35 paul15024 thank you
15:36 Jun Try to search "Get the scientific name for an organism" on the HOWTO
15:39 paul15024 i need a taxid for that to work
15:40 paul15024 i only have accession numbers
15:41 paul15024 bbl
15:56 Jun Hi, paul15024. I think using Bio::DB::EUtilities is the best way to do that
15:57 Jun Just check the example, if you have an id, say $id
15:57 Jun my $factory = Bio::DB::EUtilities->new(-eutil => 'efetch',
15:57 Jun -db    => 'taxonomy',
15:57 Jun -email => 'mymail@foo.bar',
15:57 Jun -id    => [$id] );
15:57 Jun Ok, the code doesnot look good here.
15:57 Jun But I think the HOWTO has provided a good example...
15:58 Jun Try to spend some time on it, actually it took me 1hr to understand what is going on with this module :P
16:00 Jun In your case, you may need to use "efetch" to get the taxid for taxonomy, then use "esummary" to get scientific name of the taxid.
16:16 paul15024 does 'id' have to be a GI number or can it be an accession number?
16:26 Jun usually id means gi number
16:27 Jun so you should convert your accession J02400 to gi first
16:44 Jun Get to go now. paul15024, I think what you can do is, first, convert your accession to gi using "esearch", then find the taxid from gi using "esummary", after that, you use "efetch" to get the scientific name from the taxid
16:46 Jun If you are not in a hurry, you can visit the Bio::DB::EUtilities HOWTO in BioPerl later next week, I can add this into the HOWTO
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