[Bioperl-l] Problems parsing Accesion number in FASTA format.

[David García Cortés]

Thank you very much. Now it works!!!! :-)

----- Original Message ----- 
From: "Jason Stajich" <jason.stajich at duke.edu>
To: "David García Cortés" <davidg at lsi.upc.edu>
Cc: <bioperl-l at bioperl.org>
Sent: Monday, January 03, 2005 6:18 PM
Subject: Re: [Bioperl-l] Problems parsing Accesion number in FASTA format.


>I though someone was going to centralize this function at some point. 
>Right now there is a _get_accession_version function in 
>Bio::SearchIO::blast.  Perhaps someone would care to make a utility  module 
>which can export a bunch of useful functions like this?
>
> my $seqsfich  = Bio::SeqIO->new(-file=>"nr.fa", '-format' => 'Fasta');
>
>  while (my $seq = $seqsfich->next_seq()) {
> my ($acc,$ver) = &_get_accession_version($seq->display_id)
> $seq->accession_number($acc);
> $seq->version($ver);
>          print STDOUT "Sequence accession number: ", 
> $seq->accession_number, "\n";
>  }
>
> sub _get_accession_version {
>     my $id = shift;
>
>     # handle case when this is accidently called as a class method
>     if( ref($id) && $id->isa('Bio::SearchIO') ) {
>         $id = shift;
>     }
>     return undef unless defined $id;
>     my ($acc, $version);
>     if ($id =~ /(gb|emb|dbj|sp|pdb|bbs|ref|lcl)\|(.*)\|(.*)/) {
>         ($acc, $version) = split /\./, $2;
>     } elsif ($id =~ /(pir|prf|pat|gnl)\|(.*)\|(.*)/) {
>         ($acc, $version) = split /\./, $3;
>     } else {
>         #punt, not matching the db's at 
> ftp://ftp.ncbi.nih.gov/blast/db/README
>         #Database Name                     Identifier Syntax
>         #============================      ========================
>         #GenBank                           gb|accession|locus
>         #EMBL Data Library                 emb|accession|locus
>         #DDBJ, DNA Database of Japan       dbj|accession|locus
>         #NBRF PIR                          pir||entry
>         #Protein Research Foundation       prf||name
>         #SWISS-PROT                        sp|accession|entry name
>         #Brookhaven Protein Data Bank      pdb|entry|chain
>         #Patents                           pat|country|number
>         #GenInfo Backbone Id               bbs|number
>         #General database identifier           gnl|database|identifier
>         #NCBI Reference Sequence           ref|accession|locus
>         #Local Sequence identifier         lcl|identifier
>         $acc=$id;
>     }
>     return ($acc,$version);
> }
>
> On Jan 3, 2005, at 12:00 PM, David García Cortés wrote:
>
>> Hello.
>>
>> I have the "nr" database in FASTA format (downloaded from NCBI  website), 
>> and i want to retrieve the accession number of each sequence  in that 
>> database, so I do the following:
>>
>> my $seqsfich  = Bio::SeqIO->new(-file=>"nr.fa", '-format' => 'Fasta');
>>
>>  while (my $seq = $seqsfich->next_seq()) {
>>     print STDOUT "Sequence accession number: ", $seq->accession, "\n";
>>    }
>>
>> But the results I get are:
>>
>> Sequence accession number: unknown
>> Sequence accession number: unknown
>> Sequence accession number: unknown
>> Sequence accession number: unknown
>> etc...
>>
>> Here you can see a fragment of the "nr.fa" file
>> :
>>> gi|2695847|emb|CAA73704.1| immunoglobulin heavy chain [Acipenser 
>>> baerii]
>> MGILTALCIIMTALSSVRSDVVLTESGPAVIKPGESHKLSCKASGFTFSSAYMSWVRQAPGKGLEWVAYIY 
>> SGGSSTYYA
>> QSVQGRFAISRDDSNSMLYLQMNSLKTEDTAVYYCARGGLGWSLDYWGKGTMITVTSATPSPPTVFPLMES 
>> CCLSDISGP
>> VATGCLATGFCLPPRPSRGLINLEKL
>>> gi|2695851|emb|CAA73709.1| immunoglobulin heavy chain [Acipenser 
>>> baerii]
>> MGILTALCIIMTALSSVRSDVVLTESGPAVVKPGESHKLSCKAAGFTFSSYWMGWVRQTPGKGLEWVSIIS 
>> AGGSTYYAP
>> SVEGRFTISRDNSNSMLYLQMNSLKTEDTAMYYCARKPETGSYGNISFEHWGKGTMITVTSATPSPPTVFP 
>> LMQACCSVD
>> VTGPSATGCLATEF
>>> gi|2695853|emb|CAA73712.1| immunoglobulin heavy chain [Acipenser 
>>> baerii]
>> MGILTALCIIMTALSSVRSDVVLTESGPAVIKPGESHKLSCKASGFTFSSNNMGWVRQAPGKGLEWVSTIS 
>> YSVNAYYAQ
>> SVQGRFTISRDDSNSMLYLQMNSLKTEDSAVYYCARESNFNRFDYWGSGTMVTVTNATPSPPTVFPLMQAC 
>> CSVDVTGPS
>> ATGCLATEF
>>
>> I suppose the accession numbers are: CAA73704.1, CAA73709.1, 
>> CAA73712.1|, etc... (¿?)
>> The thing is, how can I do for Bioperl to parse and recognize them?
>>
>> Thanks in advance.
>>
>> --
>> David García Cortés
>> Instituto Nacional de Bioinformática (INB)
>> Nodo Computacional GNHC-2 UPC-CIRI
>> c/. Jordi Girona 1-3
>> Modul C6-E201                   Tel.  : 934 011 650
>> E-08034 Barcelona               Fax   : 934 017 014
>> Catalunya (Spain)               e-mail: davidg at lsi.upc.edu
>>
>>
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>>
>>
> --
> Jason Stajich
> jason.stajich at duke.edu
> http://www.duke.edu/~jes12/
>
>