Ewan Birney

NAME

Bio::LiveSeq::IO::Loader - Parent Loader for LiveSeq

SYNOPSIS

  #documentation needed

DESCRIPTION

This package holds common methods used by BioPerl, SRS and file loaders. It contains methods to create LiveSeq objects out of entire entries or from a localized sequence region surrounding a particular gene.

AUTHOR - Joseph A.L. Insana

Email: Insana@ebi.ac.uk, jinsana@gmx.net

Address:

     EMBL Outstation, European Bioinformatics Institute
     Wellcome Trust Genome Campus, Hinxton
     Cambs. CB10 1SD, United Kingdom 

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

entry2liveseq

  Title   : entry2liveseq
  Usage   : @translationobjects=$loader->entry2liveseq();
          : @translationobjects=$loader->entry2liveseq(-getswissprotinfo => 0);
  Function: creates LiveSeq objects from an entry previously loaded
  Returns : array of references to objects of class Translation
  Errorcode 0
  Args    : optional boolean flag to avoid the retrieval of SwissProt
            informations for all Transcripts containing SwissProt x-reference
            default is 1 (to retrieve those informations and create AARange
            LiveSeq objects)
  Note    : this method can get really slow for big entries. The lightweight
            gene2liveseq method is recommended

novelaasequence2gene

  Title   : novelaasequence2gene
  Usage   : $gene=$loader->novelaasequence2gene(-aasequence => "MGLAAPTRS*");
          : $gene=$loader->novelaasequence2gene(-aasequence => "MGLAAPTRS*");
                                             -taxon => 9606,
                                             -gene_name => "tyr-kinase");

  Function: creates LiveSeq objects from a novel amino acid sequence,
            using codon usage database to choose codons according to
            relative frequencies.
            If a taxon ID is not specified, the default is to use the human
            one (taxonomy ID 9606).
  Returns : reference to a Gene object containing references to LiveSeq objects
  Errorcode 0
  Args    : string containing an amino acid sequence
            integer (optional) with a taxonomy ID
            string specifying a gene name

gene2liveseq

  Title   : gene2liveseq
  Usage   : $gene=$loader->gene2liveseq(-gene_name => "gene name");
          : $gene=$loader->gene2liveseq(-gene_name => "gene name",
                                        -flanking => 64);
          : $gene=$loader->gene2liveseq(-gene_name => "gene name",
                                        -getswissprotinfo => 0);
          : $gene=$loader->gene2liveseq(-position => 4);

  Function: creates LiveSeq objects from an entry previously loaded
            It is a "light weight" creation because it creates
            a LiveSequence just for the interesting region in an entry
            (instead than for the total entry, like in entry2liveseq) and for
            the flanking regions up to 500 nucleotides (default) or up to
            the specified amount of nucleotides (given as argument) around the
            Gene.
  Returns : reference to a Gene object containing possibly alternative
            Transcripts.
  Errorcode 0
  Args    : string containing the gene name as in the EMBL feature qualifier
            integer (optional) "flanking": amount of flanking bases to be kept
            boolean (optional) "getswissprotinfo": if set to "0" it will avoid
             trying to fetch information from a crossreference to a SwissProt
             entry, avoding the process of creation of AARange objects
             It is "1" (on) by default

            Alternative to a gene_name, a position can be given: an
            integer (1-) containing the position of the desired CDS in the
            loaded entry

printswissprot

  Title   : printswissprot
  Usage   : $loader->printswissprot($hashref);
  Function: prints out all informations loaded from a database entry into the
            loader. Mainly used for testing purposes.
  Args    : a hashref containing the SWISSPROT entry datas
  Note    : the hashref can be obtained with a call to the method
               $loader->get_swisshash()      (only with SRS loader or
                                              BioPerl via Bio::DB::EMBL.pm)
            that takes as argument a string like "SWISS-PROT:P10275" or
            from $loader->swissprot2hash() that takes an SRS query string
            as its argument (e.g. "swissprot-acc:P10275")

printembl

  Title   : printembl
  Usage   : $loader->printembl();
  Function: prints out all informations loaded from a database entry into the
            loader. Mainly used for testing purposes.
  Args    : none

genes

  Title   : genes
  Usage   : $loader->genes();
  Function: Returns an array of gene_names (strings) contained in the loaded
            entry.
  Args    : none