Victorian-Bioinformatics-Consortium/prokka — pull request #18 by aleimba (2014-05-30 12:55:17+00:00)
Title: Multiple EC_number tags for CDSs, lower case initials in /product descriptions for prokka-1.9.1-testing

#### New pull request to include multiple EC_number tags per CDS with version *prokka-1.9.1-testing* and some bug fixes
For this purpose the database format was adapted to include several EC_numbers separated by a **semicolon**, e.g.:
>K9NBS6 3.5.1.13;3.5.1.14;3.5.1.4~~~aam~~~Acylamidase
MTEQNLHWLSATEMAASVASNNLSPNEIAEAMIQRVDAVNPS...

This is included in the necessary database preparations scripts:
* `prokka-biocyc_to_fasta_db`
* `prokka-genbank_to_fasta_db`
* `prokka-genpept_to_fasta_db`
* `prokka-hamap_to_hmm`
* `prokka-uniprot_to_fasta_db`

`prokka` can handle this format now. As a result a new uniprot database in `/db/kingdom/Bacteria/sprot` is included.

Additionally, a couple of bug fixes:
* Adapted the usage of `prokka-hamap_to_hmm` (will concatenate result files to 'HAMAP.hmm') and `prokka-uniprot_to_fasta_db` (divert stdout to '> sprot')
* /protein description initials are changed to lowercase (as instructed by NCBI), except for 'Rossman' and 'Willebrand', see https://github.com/aleimba/prokka/blob/master/bin/prokka#L1177-1178
* I didn't get the if-condition in line 58 of `prokka-uniprot_to_fasta_db`. What is 'if (1)' for? https://github.com/Victorian-Bioinformatics-Consortium/prokka/blob/master/bin/prokka-uniprot_to_fasta_db#L58
I removed the condition.
* Included Shaun's 'Remove stray space from locus_tag' #15 pull request, so there's no conflict between our pull requests

This might warrant a new version, changed it to *prokka-1.9.2.-testing*. *ChangeLog.txt* is updated as well.