HMMER2GO version 0.18.2

Summary of changes in this version:

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.

See the Changes file for more information.

HMMER2GO version 0.18.1

Summary of changes in this version:

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.

See the Changes file for more information.

HMMER2GO version 0.18.0

Summary of changes in this version:

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.

Please see the "Changes" file for more information.

HMMER2GO version 0.17.9

Summary of changes in this version:

• 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.

See the "Changes" file for more information.

HMMER2GO version 0.17.8

Summary of changes in this version:

• 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.

See the "Changes" file for more information.

HMMER2GO version 0.17.7

Summary of changes in this version:

• Add method to transform identifiers that may cause problems for EMBOSS. Added tests for the expected results of the method.

See the "Changes" file for more information.

HMMER2GO version 0.17.5

Summary of changes in this version:

• Fix bug with newlines being inserted into sequences when printing ORFs in the same frame.

See the "Changes" file for more information.

HMMER2GO version 0.17.2

Summary of changes in this version:

• 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.

See the "Changes" file for more information.

HMMER2GO version 0.17.1

Summary of changes in this version:

• Fix bug in expected Pfam mappings based on new entries.

HMMER2GO version 0.17

Summary of changes in this version:

• Remove use of spawning a new shell for executing programs.
• Add faster and more portable method for searching path for
  required programs.

See the "Changes" file for more information.