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.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, 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 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