This module is used to parse the NCBI-Taxonomy files and return lists of taxonomic lineages for a given GI.
Current version is 0.90
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To install this module type the following:
perl Makefile.PL
make
make test
make installperldoc NCBI::TaxonomyThis module requires the following other modules:
- DateTime::Format::Natural (v0.96 or above),
- version (v0.77 or above),
- Log::Log4perl (v1.29 or above),
- Storable,
- Test::More,
- Test::Exception
- no protein/nucleic acid parameter is nessesary
- Support for merged TaxIDs
- for non exstisting gis links to history tool of NCBI will be returned
- first version compatible to the CPAN standards. Template was
created using h2xs v1.23 with options:
-d -XA -n NCBI::Taxonomy- I fixed the files Changes, README, MANIFEST, but the whole module
files will be changed in the next version
- I moved the old module TaxonomyByGi to my new module NCBI::Taxonomy and changed the files Changes and README. I did not add documentation.
- added the file Changes to the version control (I forgot to add it ;) )
- TODOs:
- no tests writen
- have to fill the documentation
- I want to add the functions to download and prepare the index-files
- added a handling for GIs which could not be found in the index-file and had no substitution comment inside the Genbank Entry
- added a handler for download errors caused by NCBI requests
- A new version which uses a binary file type for storing the gi and taxid information.
- Switched to Log::Log4perl for messages and added croak commands for failing IO calls!
- I am using a ring buffer to save 6000 lineages for taxids to speed up the finding of the lineages.
- Implementation of a last common ancestor
- Include last common ancestor calculations now
- Fixed the LCA on request of Felix… A new parameter was added and an empty result array reference will be returned, if less than 2 lineages are compared.
- Included the new format for the nodes and removed the subroutines which were necessary for the import of the dmp files.
- Added data for creation of a DB and therefore enabling test
functionality. Moreover, the untested function getLCAbyGIs dies on
execution. To avoid this, the variable
$no_die_on_untested_functionscan be set to a true value on line 18!
- First version available on GitHub
- Added a licence file and a org-mode based readme file
- Badges for build and coverage are added
- First version which supports Accessions and GIs after NCBI phases out GIs
- New index file format
The MIT License (MIT)
Copyright (c) 2009-2018 Frank Förster
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
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