Humann

New Features

* Improvements to MetaCyc pathway quantification
* Refined gene families to MetaCyc reactions mapping (update ignores ECs with less than 4 levels of classification)

Cross Platform Compatibility Updates

* Modification to glpk/glpsol update version (resolves glpsol write permission errors and glpsol links to build directory)

Cross Platform Compatibility Updates

* Added new option "--build-diamond" to the install (the default for Mac OS is to build diamond)

Bug Fixes

* Updated the fastq to fasta function to allow for quality score lines that are similar to sequence lines (ie all alphabetical characters)

New Features

* Improvements to structured pathway quantification identify more pathways
* Updated databases to MetaCyc v19.1
* Added UniProt TrEMBL data to reactions mappings
* Added gap filling
* Added automated install of dependencies (bowtie2 and diamond)
* Added alert for user when running with demo databases and non-demo input file
* Added new option "--names {ko,metacyc-pwy,uniref50}" to humann2_rename_table
* Added new option "--groups {uniref50_ko,uniref50_go,uniref50_ec,uniref50_rxn}" to humann2_regroup_table
* Added new option "--output-max-decimals" to set the number of decimals written to the output files

Interface Changes

* The default mapping file format for humann2_regroup_table has been reversed (it is now groups to features)
* The humann2_rename_table option for a custom mapping file was changed from "--names" to "--custom"
* The humann2_regroup_table option for a custom mapping file was changed from "--groups" to "--custom"

Bug Fixes

* Updated fastq to fasta function to allow for "" (special fastq character) at beginning of quality score lines

Cross Platform Compatibility Updates

* Updated humann2_join_table to ignore dot files (ie .DS_Store on Apple OS X)

Cross Platform Compatibility Updates

* Added to install process the setting execute permissions on glpsol binaries
* On some platforms when glpsol is installed by setuptools it does not keep its execute permissions

New Features

* Added "--metaphlan-options"
* Allows user to set any options for MetaPhlAn2 including database locations
* Example: --metaphlan-options="-t rel_ab"
* Error message reporting has been updated to include messages from external tools
* Example: "metaphlan2.py: error: unrecognized arguments: --stat_e 1.0"
* Updated MetaCyc structured pathways database
* Removed reactions with only non-specific ECs
* Set unmappable reactions (those without links to gene families) as optional reactions
* Filtered out small pathways

Interface Changes

* Changed option names to be more general for users with custom flows
* Changed "--chocophlan" to "--nucleotide-database"
* Changed "--uniref" to "--protein-database"

Bug Fixes

* Updated function which determines file format to allow for gene tables with scientific notation

New Features

* Added MetaCyc structured pathways database
* Added structured pathways computations for abundance and coverage