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Bio-PanGenome-1.133090
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Documentation

create_pan_geneome
Create a pan genome from a set of proteome FASTA files
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

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

Other files