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Bio::LiveSeq::IO::Loader.3pm

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
             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()      (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 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