NAME

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

SYNOPSIS

#documentation needed

DESCRIPTION

This package holds common methods used by BioPerl 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

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
          information for all Transcripts containing SwissProt x-reference
          default is 1 (to retrieve those information 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, avoiding 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 information 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()      (BioPerl via Bio::DB::EMBL.pm)
	    that takes as argument a string like "SWISS-PROT:P10275"

printembl

Title   : printembl
Usage   : $loader->printembl();
Function: prints out all information 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