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Bio-MUST-Apps-FortyTwo-0.202160
River stage one • 1 direct dependent • 1 total dependent
++

Changes for version 0.202160 - 2020-08-03

  • Additions
    • 42: Optional consolidation of redundant orthologues (through CAP3 contiging)
    • 42: Support for basic multithreading (--threads command-line option)
    • 1331: Added 'off' value for aligner_mode (e.g., to extract UTRs)
  • Changes
    • 42/1331: Improved warning/error messages (prefixed by [RUN] etc)
    • 42/1331: Renamed some options in YAML file (ref_brh_mode => ref_brh, trimming_mode => trim_homologues, ali_patch_mode => ali_skip_self, ls_action => ali_keep_lengthened_seqs)
    • 42: Inverted columns in yaml-generator.pl mapper (IDM) files for consistency with Bio::MUST::Core
    • 42: Updated yaml-generator.pl to mirror option name changes
    • 42: Enabled auto-detagging of preexisting #NEW# seqs (but see ali_keep_old_new_tags)
    • 42: Improved robustness of orgs and query_orgs name checking in YAML file
  • Fixes
    • 42: Fixed bug leading to empty tax_reports in metagenomic mode
    • 42: Fixed bug where preexisting #NEW# seqs causing a "Can't call method "stringify" on an undefined value"
    • 42: Fixed bug where preexisting #NEW# seqs were removed due to wrongly detected redundancy

Documentation

compress-db.pl
Post-process assembler for transcript enrichment using 42
forty-two.pl
The Answer to the Ultimate Question of Phylogenomics
leel.pl
The Elite of the Phylogenomic Back-Translators
yaml-generator-42.pl
Interactive or batch generator for 42 YAML config files
FortyTwo::Manual
User Guide for Forty-Two

Modules

Bio::MUST::Apps::Debrief42
Main class for debrief-42 tool
Bio::MUST::Apps::Debrief42::OrgReport
Internal class for tabular tax-report parser
Bio::MUST::Apps::Debrief42::RunReport
Internal class for tabular tax-report parser
Bio::MUST::Apps::Debrief42::TaxReport
Front-end class for tabular tax-report parser
Bio::MUST::Apps::Debrief42::TaxReport::NewSeq
Internal class for tabular tax-report parser
Bio::MUST::Apps::FortyTwo
Main class for forty-two tool
Bio::MUST::Apps::FortyTwo::AliProcessor
Internal class for forty-two tool
Bio::MUST::Apps::FortyTwo::OrgProcessor
Internal class for forty-two tool
Bio::MUST::Apps::FortyTwo::RunProcessor
Internal class for forty-two tool
Bio::MUST::Apps::Leel
Main class for leel tool
Bio::MUST::Apps::Leel::AliProcessor
Internal class for leel tool
Bio::MUST::Apps::Leel::OrgProcessor
Internal class for leel tool
Bio::MUST::Apps::Leel::RunProcessor
Internal class for leel tool
Bio::MUST::Apps::Roles::AliProcable
Attributes and methods common to AliProcessor objects
Bio::MUST::Apps::Roles::Configable
Attributes and methods common to Leel and FortyTwo objects
Bio::MUST::Apps::Roles::OrgProcable
Attributes and methods common to OrgProcessor objects
Bio::MUST::Apps::Roles::RunProcable
Attributes and methods common to RunProcessor objects
Bio::MUST::Apps::SlaveAligner::Local
Internal class for slave-aligner

Other files