[Bioperl-l] [Fwd: Re: A question about iBio::Index: and its correct use]

Mark A. Jensen maj at fortinbras.us
Thu Nov 5 11:39:09 EST 2009


Yes, these are files created by the SDBM, Perl's internal db manager. You should 
be able to
open the index by simply
$inx = Bio::Index::Fasta->new('PC9.fasta.idx');
and the dbm will know what to do--
cheers MAJ
----- Original Message ----- 
From: <jluis.lavin at unavarra.es>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: <jluis.lavin at unavarra.es>; <bioperl-l at lists.open-bio.org>
Sent: Thursday, November 05, 2009 11:21 AM
Subject: Re: [Bioperl-l] [Fwd: Re: A question about iBio::Index: and its correct 
use]


> Thank you very much Mark, that´s a good point :$
> I guess your correction is referred to the second script, isn´t it?
>
> If it is so, there is still a problem with the first script, it doesn´t
> create the PC9.fasta.idx file, instead it creates two files named:
> -PC9.fasta.idx.pag
> -PC9.fasta.idx.dir
>
> which seem to be clearly related with some kind of indexing process...but,
> unless the PC9.fasta.idx file is only virtual or remains hidden, I can´t
> find it anywhere...
> Forgive me if I´m talking nosense...
>
> Thank you very much again for your help ;)
>
>
> El Jue, 5 de Noviembre de 2009, 17:02, Mark A. Jensen escribió:
>> Hey José,
>> The first thing that jumps out it the index file name. Looks
>> like you create it as
>> PC9.fasta.idx
>> But you read it as
>> PC9.fasta
>> Not an unusual mistake. Do
>> my $inx = Bio::Index::Fasta->new('PC9.fasta.idx');
>> and see if it works.
>> MAJ
>> ----- Original Message -----
>> From: <jluis.lavin at unavarra.es>
>> To: <bioperl-l at lists.open-bio.org>
>> Sent: Thursday, November 05, 2009 10:46 AM
>> Subject: [Bioperl-l] [Fwd: Re: A question about iBio::Index: and its
>> correct
>> use]
>>
>>
>>
>>
>> ---------------------------- Mensaje original ----------------------------
>> Subject: Re: [Bioperl-l] A question about iBio::Index: and its correct use
>> From:    jluis.lavin at unavarra.es
>> Fecha:   Jue, 5 de Noviembre de 2009, 16:46
>> To:      "Mark A. Jensen" <maj at fortinbras.us>
>> --------------------------------------------------------------------------
>>
>> Hi Mark,
>>
>> I´ve actually got two scripts, the first one is to create the index and
>> the second one is to retrieve the sequence lis from the indexed file.
>>
>> 1)Here is the Index creation script:
>>
>> #!/c:/Perl -w
>> use strict;
>> use Bio::Index::Fasta;
>> use strict;
>>
>> print "Enter file for indexing: \n";
>> my $Index_File_Name = <STDIN>;
>> my $inx = Bio::Index::Fasta->new(-filename => $Index_File_Name.".idx",
>>     -write_flag => 1);
>> $inx->make_index(my $File_Name);
>>
>> 2)And here is the sequence retrieval script:
>>
>> #!/c:/Perl -w
>> use Bio::Index::Fasta;
>> use strict;
>> #PC9.fasta is my genomic file
>> my $Index_File_Name ="PC9.fasta";
>> my $inx = Bio::Index::Fasta->new($Index_File_Name);
>> #LCS.txt is my sequences list
>> @ARGV = <lCS.txt>;
>> foreach  my $id (@ARGV) {
>> if ($id eq ''){
>> die ("empty list")
>> }
>> else {
>> my $seqobj = $inx->fetch($id);
>> my $out = new Bio::SeqIO (-file => ">>extracted_seqs.fasta",
>> -format => 'fasta');
>> $out->write_seq($seqobj);
>> }
>> }
>> exit;
>> }
>>
>> I hope this code is not a total scum...
>>
>> Thanks in advance ;)
>>
>>
>>
>> El Jue, 5 de Noviembre de 2009, 16:39, Mark A. Jensen escribió:
>>> José -- It looks like this is a good solution to your problem. Please
>>> send
>>> you
>>> script so we can look at it-
>>> cheers Mark
>>> ----- Original Message -----
>>> From: <jluis.lavin at unavarra.es>
>>> To: <bioperl-l at lists.open-bio.org>
>>> Sent: Thursday, November 05, 2009 10:28 AM
>>> Subject: [Bioperl-l] A question about iBio::Index: and its correct use
>>>
>>>
>>>
>>> Hello to all,
>>>
>>> I´m trying to write a script to retrieve a list of sequences from a
>>> local
>>> FASTA file (for example a fasta archive where all the protein models of
>>> an
>>> organism are stored). This file would be used by me as some kind "local
>>> database" (sorry if I mistake a few concepts...)
>>> I´ve been reading the BioPerl HOWTOs and I came across the
>>> Bio::Index::Fasta tool.
>>> If I didn´t misunderstood what I read (which can be easy because my low
>>> level on programming) this Indexing tool should do the job.
>>> I wrote a couple of scripts based on the documentation i read about this
>>> tool, but I don´t seem to be able to create the index file to be used
>>> later (to retrieve the sequences from).
>>> -First of all, I want to ask the people in this forum if the
>>> Bio::Index::Fasta is the right one to chose for this tasks.
>>> -Then I´ll beg you to take a look at my scripts, because I don´t seem to
>>> catch the bug...
>>>
>>> Best wishes to you all and thanks in advance ;)
>>>
>>> --
>>> José Luis Lavín Trueba, PhD
>>>
>>> Dpto. de Producción Agraria
>>> Grupo de Genética y Microbiología
>>> Universidad Pública de Navarra
>>> 31006 Pamplona
>>> Navarra
>>> SPAIN
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>>
>>
>>
>> --
>> Dr. José Luis Lavín Trueba
>>
>> Dpto. de Producción Agraria
>> Grupo de Genética y Microbiología
>> Universidad Pública de Navarra
>> 31006 Pamplona
>> Navarra
>> SPAIN
>>
>>
>>
>> --
>> Dr. José Luis Lavín Trueba
>>
>> Dpto. de Producción Agraria
>> Grupo de Genética y Microbiología
>> Universidad Pública de Navarra
>> 31006 Pamplona
>> Navarra
>> SPAIN
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
>
>
> -- 
> Dr. José Luis Lavín Trueba
>
> Dpto. de Producción Agraria
> Grupo de Genética y Microbiología
> Universidad Pública de Navarra
> 31006 Pamplona
> Navarra
> SPAIN
>
>
>
> 



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