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Bio::LiveSeq::IO::LoadUser)Contributed Perl DocumenBio::LiveSeq::IO::Loader(3)

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

perl v5.14.1			  2011-07-22	   Bio::LiveSeq::IO::Loader(3)
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