** Description
This module is used to parse the NCBI-Taxonomy files and return lists
of taxonomic lineages for a given GI.
** Version
Current version is 0.90
** Build
** Coverage
** Installation
To install this module type the following:
+BEGIN_SRC sh
perl Makefile.PL
make
make test
make install
+END_SRC
** Documentation
+BEGIN_SRC sh
perldoc NCBI::Taxonomy
+END_SRC
** Dependencies
This 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
History
** Version 0.1
Version 0.2
*** Version 0.3
- no protein/nucleic acid parameter is nessesary
*** Version 0.4
- Support for merged TaxIDs
- for non exstisting gis links to history tool of NCBI will be
returned
*** Version 0.5
- first version compatible to the CPAN standards. Template was
created using h2xs v1.23 with options:
+BEGIN_SRC sh
-d -XA -n NCBI::Taxonomy
+END_SRC
- I fixed the files Changes, README, MANIFEST, but the whole module
files will be changed in the next version
*** Version 0.51
- 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
*** Version 0.511
- added a handling for GIs which could not be found in the
index-file and had no substitution comment inside the Genbank
Entry
*** Version 0.52
- added a handler for download errors caused by NCBI requests
*** Version 0.60.0
- A new version which uses a binary file type for storing the gi and taxid information.
*** Version 0.61.1853
- Switched to Log::Log4perl for messages and added croak commands for failing IO calls!
*** Version 0.62.1854
- I am using a ring buffer to save 6000 lineages for taxids to speed
up the finding of the lineages.
** Version 0.63.
- Implementation of a last common ancestor
**** Version 0.63.1863
- Include last common ancestor calculations now
*** Version 0.64.1868
- 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.
*** Version 0.70.3
- Included the new format for the nodes and removed the subroutines
which were necessary for the import of the dmp files.
*** Version 0.70.5
-
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
+BEGIN_SRC perl
$no_die_on_untested_functions
+END_SRC
can be set to a true value on line 18!
*** Version 0.80.0
- First version available on [[https://github.com/greatfireball/NCBI-Taxonomy][GitHub]]
- Added a licence file and a org-mode based readme file
- Badges for build and coverage are added
*** Version 0.90.0
- First version which supports Accessions and GIs after NCBI phases out GIs
- New index file format
** Copyright and licence
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.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.