Bio::LiveSeq::IO::Loader - Parent Loader for LiveSeq #documentation needed 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. Email: Insana@ebi.ac.uk, jinsana@gmx.net Address: EMBL Outstation, European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambs. CB10 1SD, United Kingdom 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