[Bioperl-l] retrieve refseq ids from UIDs

[Smithies, Russell]

I assume you've had a look at the cookbook http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook
Also take a look at elink, it might do what you are after http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook#I_want_a_list_of_database_.27x.27_UIDs_that_are_linked_from_a_list_of_database_.27y.27_UIDs
The Scrapbook is a good place to get ideas as well http://www.bioperl.org/wiki/Category:Scrapbook



--Russell

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Carnë Draug
> Sent: Tuesday, 28 June 2011 1:46 p.m.
> To: bioperl mailing list
> Subject: [Bioperl-l] retrieve refseq ids from UIDs
> 
> Hi
> 
> I've been having some trouble with bioperl and I was hoping that
> someone could help me. I'm trying to obtain the transcript and protein
> id of RefSeq given a gene UID. For example, for the gene with UID 9555
> http://www.ncbi.nlm.nih.gov/gene/9555 I'd like to get the transcripts
> and proteins ids as in the section (NCBI Reference Sequence (RefSeq))
> of that page, the ones like:
> 
> NM_001040158.1 → NP_001035248.1  core histone macro-H2A.1 isoform 2
> NM_004893.2 → NP_004884.1  core histone macro-H2A.1 isoform 2
> 
> I believe to be fairly good with perl, just not with bioperl yet.
> Currently, what I'm doing is after getting the UIDs, using EUtilities
> esummary to get the genomic coordinates, then use efecth to extract
> that sequence and parse it to obtain the protein_id and transcript_id.
> Until now it's ok because I actually wanted all those things but now
> I'd like to skip the first parts and get only the transcripts or
> proteins. I'm sure there must be a "smarter" way to do this.
> 
> I've tried to use efetch, suply the UID as id and use
> get_Response->content which gives me a some kind of structure with the
> info that I want but how do access it properly? Like this
> 
> my @ids = qw(9555);
> my $factory = Bio::DB::EUtilities->new(-eutil   => 'efetch',
>                                        -db      => 'gene',
>                                        -id      => \@ids,
>                                        );
> say $factory->get_Response->content;
> 
> Also, when using the einfo script that comes with bioperl, to get the
> info I should be able to get when searching the database gene (running
> as einfo -d=gene), it says that I should be able to get it. At least
> one of the fields is the following:
> 
> Field Code          :ACCN
> Field Name          :Nucleotide/Protein Accession
> Description         :Nucleotide or protein accession(s) associated
> with this gene
> Term Count          :49104652
> Attributes          :is_singletoken
> 
> How do I get to this field?
> 
> When using esummary to get a docum and then use the to_string method,
> I still can't see anything useful.
> 
>   my $summaries = Bio::DB::EUtilities->new(
>                                             -eutil  => 'esummary',
>                                             -db     => 'gene',
>                                             -id     => \@ids,
>                                           );
> 
>   while (my $docsum = $summaries->next_DocSum) {
>     say $docsum->to_string();
>   }
> 
> Any help would be very appreciated. Thanks in advance,
> Carnë Draug
> 
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> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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