Andrew Page > Bio-AutomatedAnnotation

Bio-AutomatedAnnotation

This Release Bio-AutomatedAnnotation-1.133090  [Download] [Browse 05 Nov 2013
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Repository https://github.com/sanger-pathogens/Bio-AutomatedAnnotation.git
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License The GNU General Public License, Version not specified
Special Files
LICENSE
Makefile.PL
MANIFEST
META.yml
README

Modules

Bio::AutomatedAnnotation Automated annotation of assemblies      
Bio::AutomatedAnnotation::CommandLine::AnnotateBacteria provide a commandline interface to the annotation wrappers      
Bio::AutomatedAnnotation::CommandLine::GeneNameOccurances Create a spreadsheet with gene name occurances      
Bio::AutomatedAnnotation::CommandLine::ParseGenesFromGFFs provide a commandline interface to pull out genes from multiple GFF files      
Bio::AutomatedAnnotation::Exceptions Exceptions for input data      
Bio::AutomatedAnnotation::External::Cmscan Run and parse the output of cmscan      
Bio::AutomatedAnnotation::GeneNameOccurances Parse the gene names from multiple GFF files and provide a matrix of matches.      
Bio::AutomatedAnnotation::GeneNamesFromGFF Parse a GFF and efficiently extract out the Gene Names      
Bio::AutomatedAnnotation::ParseGenesFromGFF Parse a GFF file and efficiency extract the gene sequence.      
Bio::AutomatedAnnotation::ParseGenesFromGFFs Parse GFF files and efficiency extract the gene sequence.      
Bio::AutomatedAnnotation::Prokka Prokka class for bacterial annotation      
Bio::AutomatedAnnotation::SpreadsheetOfGeneOccurances Output a spreadsheet with the gene occurances per file      

Documentation

annotate_bacteria Annotate some bacteria  
gene_name_occurances Create a spreadsheet with gene name occurances  
parse_genes_from_gffs Parse genes out of gff files