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