Andrew Page > Bio-PanGenome-1.133090

Bio-PanGenome-1.133090

This Release Bio-PanGenome-1.133090  [Download] [Browse 05 Nov 2013
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Repository https://github.com/sanger-pathogens/Bio-PanGenome.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::PanGenome Create a pan genome      
Bio::PanGenome::AnalyseGroups Take in a groups file and the original FASTA files and create plots and stats      
Bio::PanGenome::AnnotateGroups Take in a group file and assosiated GFF files for the isolates and update the group name to the gene name      
Bio::PanGenome::ChunkFastaFile Take in a FASTA file and chunk it up into smaller pieces.      
Bio::PanGenome::ClustersRole A role to read a clusters file from CD hit      
Bio::PanGenome::CombinedProteome Take in multiple FASTA sequences containing proteomes and concat them together and output a FASTA file, filtering out more than 5% X's      
Bio::PanGenome::CommandLine::CreatePanGenome Take in FASTA files of proteins and cluster them      
Bio::PanGenome::CommandLine::ExtractProteomeFromGff Take in GFF files and output the proteome      
Bio::PanGenome::CommandLine::PanGenomePostAnalysis Perform the post analysis on the pan genome      
Bio::PanGenome::CommandLine::PanGenomeReorderSpreadsheet Take in a tree and a spreadsheet and output a reordered spreadsheet      
Bio::PanGenome::CommandLine::ParallelAllAgainstAllBlastp Take in a FASTA file of proteins and blast against itself      
Bio::PanGenome::CommandLine::PlotPanGenomeGroups Take in the groups file and output some summary plots      
Bio::PanGenome::CommandLine::QueryPanGenome Take in a groups file and the protein fasta files and output selected data      
Bio::PanGenome::CommandLine::TransferAnnotationToGroups Take in a groups file and a set of GFF files and transfer the consensus annotation      
Bio::PanGenome::Exceptions Exceptions for input data      
Bio::PanGenome::External::Blastp Wrapper around NCBIs blastp command      
Bio::PanGenome::External::Cdhit Wrapper to run cd-hit      
Bio::PanGenome::External::Makeblastdb Wrapper around NCBIs makeblastdb command      
Bio::PanGenome::External::Mcl Wrapper around MCL which takes in blast results and outputs clustered results      
Bio::PanGenome::External::Muscle Wrapper around Muscle for sequence alignment      
Bio::PanGenome::External::PostAnalysis Perform the post analysis      
Bio::PanGenome::External::Segmasker Wrapper around Segmasker for low complexity filtering      
Bio::PanGenome::ExtractProteomeFromGFF Take in a GFF file and create protein sequences in FASTA format      
Bio::PanGenome::ExtractProteomeFromGFFs Take in GFF files and create protein sequences in FASTA format      
Bio::PanGenome::FilterFullClusters Take an a clusters file from CD-hit and the fasta file and output a fasta file without full clusters      
Bio::PanGenome::FilterUnknownsFromFasta Take in fasta files, remove sequences with too many unknowns and return a list of the new files      
Bio::PanGenome::GeneNamesFromGFF Parse a GFF and efficiently extract ID -> Gene Name      
Bio::PanGenome::GroupLabels Add labels to the groups      
Bio::PanGenome::GroupStatistics Add labels to the groups      
Bio::PanGenome::InflateClusters Take the clusters file from cd-hit and use it to inflate the output of MCL      
Bio::PanGenome::JobRunner::LSF Execute a set of commands using LSF      
Bio::PanGenome::JobRunner::Local Execute a set of commands locally      
Bio::PanGenome::JobRunner::Role A role to add job runner functionality      
Bio::PanGenome::Output::DifferenceBetweenSets Given two sets of isolates and a group file, output whats unique in each and whats in common      
Bio::PanGenome::Output::GroupMultifasta Take in a group and create a multifasta file      
Bio::PanGenome::Output::GroupTabFiles Take in an array of files and output raw tab files for analysis by R to turn into plots      
Bio::PanGenome::Output::GroupsMultifastaNucleotide Take in a GFF files and a groups file and output one multifasta file per group with nucleotide sequences.      
Bio::PanGenome::Output::GroupsMultifastas Take in a list of groups and create multifastas files for each group      
Bio::PanGenome::Output::GroupsMultifastasNucleotide Take in a set of GFF files and a groups file and output one multifasta file per group with nucleotide sequences.      
Bio::PanGenome::Output::NumberOfGroups Create raw output files of group counts for turning into plots      
Bio::PanGenome::Output::OneGenePerGroupFasta Output a fasta file with one gene per group      
Bio::PanGenome::Output::QueryGroups Output the groups of the union of a set of input isolates      
Bio::PanGenome::ParallelAllAgainstAllBlast Run all against all blast in parallel      
Bio::PanGenome::Plot::FreqOfGenes Take in an array of frequencies of groups and output a plot      
Bio::PanGenome::PostAnalysis Post analysis of pan genomes      
Bio::PanGenome::PrepareInputFiles Take in a mixture of FASTA and GFF input files and output FASTA proteomes only      
Bio::PanGenome::ReorderSpreadsheet Take in a tree file and a spreadsheet and output a spreadsheet with reordered columns      
Bio::PanGenome::SampleOrder Take in a tree file and return an ordering of the samples      
Bio::PanGenome::SequenceLengths Take in a fasta file and create a hash with the length of each sequence      

Documentation

create_pan_geneome Create a pan genome from a set of proteome FASTA files  
create_plots.R Create R plots  
extract_proteome_from_gff Take in GFF files and output the proteome  
pan_genome_post_analysis Perform the post analysis on the pan genome  
pan_genome_reorder_spreadsheet Take in a tree and a spreadsheet and output a reordered spreadsheet  
parallel_all_against_all_blastp Take in a FASTA file of proteins and blast against itself  
plot_pan_genome_groups Take in the groups file and output some summary plots  
query_pan_genome Take in a groups file and the protein fasta files and output selected data  
transfer_annotation_to_groups Take in a groups file and a set of GFF files and transfer the consensus annotation  

Other Files

README.md