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Revision history for HMMER2GO
Version Date Location
0.18.3 06/11/2022 Saskatoon, SK
Bug fixes:
- Check for dependencies in Makefile.PL. Fixes #30.
0.18.2 03/19/2022 Vancouver, BC
Bug fixes:
- Update new Pfam URLs that use https.
New features:
- Drop travis in favor of github actions for running test suite.
- Update Perl deps for fetching data or searching over https.
0.18.1 01/09/2022 Saskatoon, SK
Bug fixes:
- Drop old FTP location of mapping files and GO ontology in favor of new location (fixes #25).
- Adjust test output for creating custom HMM database based on term search (update expected model number for the search).
New features:
- Use HTTP GET for fetching mapping and ontology files instead of FTP.
0.18.0 01/30/2021 Saskatoon, SK
Bug fixes:
- Keep the original sequence IDs in the output from 'hmmer2go getorf' without the ORF number and location
appended to the ID. Fixes issue #23.
- Omit obsolete terms from GO when writing GAF file with 'hmmer2go map2gaf' command.
- Drop usage of 'each %hash' syntax because 'keys %hash' is safer.
New features:
- Add method to get the taxon ID from NCBI based on the input species name, rather than hard coding an ID.
- For the 'hmmer2go map2gaf' command, add GAF header describing the date of the analysis, HMMER2GO version,
and the GO database version used to generate the data.
- Get GO definitions from latest full GO database (i.e., go.obo) instead of the older GO alt-ids file that was being
used for the term mapping.
0.17.9 04/19/2019 Vancouver, BC
- Change search of PATH for programs to take the first occurrence of program instead of last.
Suggestion on github issue #16.
- Add Docker image usage instructions and expand install methods.
0.17.8 05/25/2018 Vancouver, BC
- Bug fix for #15 with trying to dereference a scalar. This was caused by a changing the return value of
a method and not handling the change in the code.
0.17.7 03/29/2018 Vancouver, BC
- Add method to transform identifiers that may cause problems for EMBOSS. Added tests for the expected
results of the method.
0.17.6 01/09/2018 Vancouver, BC
- Add option to only report one ORF with the 'getorf' command when multiple ORFs have the same max
length.
- Remove use of 'each' on hash in 'getorf' command in favor of the more stable 'keys' function.
0.17.5 10/04/2017 Vancouver, BC
- Fix bug with newlines being inserted into sequences when printing ORFs in the same frame.
0.17.4 05/02/2017 Vancouver, BC
- Fix regex for getting database number with 'pfamsearch' command (resolves #11).
- Use lexical file handles everywhere.
- Test that we can open file handles everywhere.
0.17.3 09/17/2016 Vancouver, BC
- Add --outfile flag to 'run' command to make the usage a bit easier to understand
since the output is required by other commands.
0.17.2 03/02/2016 Vancouver, BC
- Fix bug in output of wrong type of ORF (previously only generating translated ORFs).
- Fix syntax error in getorf tests that was keeping all the input files from being tested.
- Add warning for getorf command for cases where multiple ORFs have the max length.
0.17.1 01/21/2016 Vancouver, BC
- Fix bug in expected Pfam mappings based on new entries.
0.17 11/02/2015 Vancouver, BC
- Remove use of spawning a new shell for executing programs.
- Add faster and more portable method for searching path for
required programs.
0.16 8/07/2015 Vancouver, BC
- Remove use of environment variables to build and install package.
0.15 6/10/2015 Vancouver, BC
- Fix bug in reporting Pfam search results for multiword search terms.
0.14 6/02/2015 Vancouver, BC
- Fix test resuls for Pfam search based on new entries in Pfam.
- Modify tests to use the latest HMMER binaries instead of an older version from the package manager
(which is incompatible with the latest models).
0.13 4/28/2015 Vancouver, BC
- Remove readfq library and fall back to supporting only FASTA format.
This is to fix issues with some sequence files generating warnings
during parsing (fixed now).
0.12 3/25/2015 Vancouver, BC
- Add compressed file support in the 'run' and 'getorf' command
classes.
- Bugfixes for the latest GO mappings in the tests for the 'mapterms'
command, and a minor fix in testing the output of the main command.
0.11 1/27/2015 Vancouver, BC
- Bugfix for the use of split in the mapterms command class.
This fixes #4 on Github.
0.10 11/05/2014 Vancouver, BC
- Add methods to automatically retry attempts to fetch
mapping file.
0.09 10/29/2014 Vancouver, BC
- Remove use of libwww in favor of net-ftp, which
has no dependencies.
- Fix dependencies listed in cpanfile and Makefile.PL.
0.08 10/13/2014 Vancouver, BC
- Modify method for formatting HMM database to use core
module (use 'File::Find' instead of 'File::Find::Rule'. The
latter module is very good, it's just not a core module).
0.07 10/11/2014 Vancouver, BC
- Add method (and tests) for formatting custom HMM database for HMMER.
- Add better error handling and reporting when running HMMER.
- Add tests for running HMMER on custom DB created with 'pfamsearch'
command.
0.06 10/03/2014 Vancouver, BC
- Add command for search Pfam for terms (called 'pfamsearch'),
and create a database of HMMs from the search results, optionally.
- Add method to 'mapterms' class to get pfam to GO mapping file
automatically, thus avoiding the requirement for a user-supplied
file.
- Change name of 'search' command to 'run' and add --program
option to allow add more domin-finding methods in the future.
0.05 08/22/2014 Vancouver, BC
- Lower Perl version requirements to 5.10 (was 5.12).
- Expanded tests to cover newer (i.e., 5.20) and older (i.e,
5.10) Perls.
0.04 08/20/2014 Vancouver, BC
- Fixed bug with not calculating the number of GO terms
correctly (was underrepresenting the actual count).
- Fixed bug with GO description being truncated in the output.
- Removed use of UTF-8 characters for generating hash keys.
- This resulted in speed improvements, and will allow the
Perl version requirement to be lowered in a future release.
- Add tests to make sure the correct results are reported when
mapping GO terms, instead of just testing that there is
output.
0.03 08/01/2014 Vancouver, BC
- Add option to find all ORFs, not just the longest.
- Bug fixes to POD in several modules.
- Update Wiki and documentation for new option.
0.02 06/10/2014 Athens, GA
- Change name of 'fetch' command to 'fetchmap' to be
more expressive.
- Make option to specify a file mandatory for the
'fetchmap' command so there is a consist usage for
all commands.
- Add documentation for main application.
- Add short option for getting documentation for all
commands.
0.01 06/09/2014 Athens, GA
- Initial release.