Mpwt 0.5.4

[ArnaudBelcour]

Add:

• support to .gbff extension for genbank files (issue #39).
• an option to use pathway prediction score of Pathway Tools (issue #42).
• a logger for mpwt (look at For developer for more informations).
• a check for ptools-init.dat file.

Fix:

• issue when checking the input files (issue #37).
• issue when checking the existence of taxon_id.tsv (issue #38).
• issue if there is multiple files in the same input folder (issue #40).
• mpwt killing Pathway Tools process to create attribute-values files even if there is only a not fatal error (issue #41).
• numerous issues with to_pf (issue #30). Add DBLINK and a check for gene name length. Rewrite how CDS and RNAs are handled. But this option needs more testing and modification in 0.5.5.
• typos in Readme.

Modify:

• pwt_wrapper: refactoring the code and add a new log (pwt_terminal.log) containing Pathway Tools log from the terminal.

Check:

• no_download_articles/--nc option is currently not working.