Mpwt

Fix:

- wrong argument number given in the fix of the error with --clean when used with -v and --cpu (issue 20).

Fix:

- error with --clean when used with -v and --cpu (issue 20).
- error if PathoLogic build is aborted (issue 22).
- typos.

Fix:

- issue with BioPAX/dat creation (issue 17).
- issue with error report with BioPAX/dat creation.

Modification:

- use by default 1 CPU, instead of using all CPUs available.

Fix:

- error with outdated argument in cleaning_input.
- several typos.

Add:

- logging instead of print (issue 12 ).
- mpwt can create BioPAX/attribute-values files when PGDBs are already in ptools-local but not in output folder (issue 13 ). In the same run, mpwt can launch PathoLogic on a set of species having no PGDBs and then launch BioPAX/attribute-values files creation on this set of species and on other species with PGDBs but with no results in the output folder.
- fatal errors from pathologic.log are now printed (issue 14 ).

Fix:

- number_cpu argument not used by cleaning function.

Add:

- option to use Pathway-Tools Hole-Filler (issue 9 ).
- error message if Pathway-Tools is not installed or not in PATH (issue 10 ).
- fasta requirement for GFF file (issue 7 ).

Fix:

- mpwt could take as input hidden files/folders (issue 8 ). Add test to check this case.
- issue with the name of the species output folder when giving an output folder but not an input folder.

Modification:

- remove global variables.
- version of dependencies.