GO::AnnotationProvider::AnnotationParser GO::AnnotationProvider::AnnotationParser is a Perl module that can parse a gene annotation file.
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Perl module parser annotation gene gene annotation annotation parser

GO::AnnotationProvider::AnnotationParser Description

GO::AnnotationProvider::AnnotationParser is a Perl module that can parse a gene annotation file. GO::AnnotationProvider::AnnotationParser is a Perl module that can parse a gene annotation file.SYNOPSISGO::AnnotationProvider::AnnotationParser - reads a Gene Ontology gene associations file, and provides methods by which to retrieve the GO annotations for the an annotated entity. Note, it is case insensitive, with some caveats - see documentation below. my $annotationParser = GO::AnnotationProvider::AnnotationParser->new(annotationFile => "data/gene_association.sgd"); my $geneName = "AAT2"; print "GO associations for gene: ", join (" ", $annotationParser->goIdsByName(name => $geneName, aspect => 'P')), "n"; print "Database ID for gene: ", $annotationParser->databaseIdByName($geneName), "n"; print "Database name: ", $annotationParser->databaseName(), "n"; print "Standard name for gene: ", $annotationParser->standardNameByName($geneName), "n"; my $i; my @geneNames = $annotationParser->allStandardNames(); foreach $i (0..10) { print "$geneNamesn"; }GO::AnnotationProvider::AnnotationParser is a concrete subclass of GO::AnnotationProvider, and creates a data structure mapping gene names to GO annotations by parsing a file of annotations provided by the Gene Ontology Consortium.This package provides object methods for retrieving GO annotations that have been parsed from a 'gene associations' file, provided by the gene ontology consortium. The format for the file is:Lines beginning with a '!' character are comment lines. Column Cardinality Contents ------ ----------- ------------------------------------------------------------- 0 1 Database abbreviation for the source of annotation (e.g. SGD) 1 1 Database identifier of the annotated entity 2 1 Standard name of the annotated entity 3 0,1 NOT (if a gene is specifically NOT annotated to the term) 4 1 GOID of the annotation 5 1,n Reference(s) for the annotation 6 1 Evidence code for the annotation 7 0,n With or From (a bit mysterious) 8 1 Aspect of the Annotation (C, F, P) 9 0,1 Name of the product being annotated 10 0,n Alias(es) of the annotated product 11 1 type of annotated entity (one of gene, transcript, protein) 12 1,2 taxonomic id of the organism encoding and/or using the product 13 1 Date of annotation YYYYMMDD 14 1 Assigned_by : The database which made the annotationColumns are separated by tabs. For those entries with a cardinality greater than 1, multiple entries are pipe , |, delimited.Further details can be found at:http://www.geneontology.org/doc/GO.annotation.html#fileThe following assumptions about the file are made (and should be true): 1. All aliases appear for all entries of a given annotated product 2. The database identifiers are unique, in that two different entities cannot have the same database id. Requirements: · Perl

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