Mpwt

Add:

- support for .fsa extension (issue 47).
- a license (issue 45).
- a --version argument to mpwt command-line (issue 44).
- pseudogene linked to mRNA in topf (issue 30).

Fix:

- issue with encoding in mpwt_wrapper.
- issue when --md could be used without -o argument (issue 46).

Thanks to cfrioux for her work on this release.

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](https://github.com/AuReMe/mpwt#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.

Add:

- an option to create taxon_id.tsv files from GenBank and GFF (issue 35).
- an option to use operon predictor of Pathway Tools (issue 33).
- an option to avoid downloading PubMed entries using a parameter in ptools-init.dat (added in Pathway Tools 23.5). But it needs more testing and maybe modification in 0.5.4 (issue 34).
- a test for to_pf using GenBank and GFF from test data (issue 30).
- errors and warnings counts in log files.

Fix:

- numerous issues with to_pf (issue 30). But this option needs more testing and modification in 0.5.4.
- incompatibility with Pathway Tools 23.5.
- typos in Readme.

Add:

- to_pf argument, allowing to convert GBK or GFF into PF files (issue 30). Need more polishing in 0.5.3.
- preprint citation in Readme.

Fix:

- error message when a GFF has no region feature (issue 31).

Add:

- taxon_id.tsv can be used to give other informations (element type, codon table, circularity of genome) to Pathway Tools (issue 28).

Fix:

- test not working on Pathway Tools 23.0.
- error message if user do not give an integer for the number of CPUs.

Modification:

- verbose and logging interactions.

**Warning**:
In this version, the behaviours of some arguments have been changed.
- the -r/size_reduction argument will delete PGDB inside ptools-local and compressed the results in zip (issue 26).
- the --clean argument (when used with -f/input_folder argument) will delete only PGDBs corresponding to species in the input_folder (issue 23).

Add:

- support for Pathologic Format (PF) file (issue 19).
- taxon_id.tsv file to manage taxon_id for species. With the argument --taxon-id/taxon_file argument, you can force mpwt to use taxon from taxon_id.tsv for all type of files (Genbank, GFF or PF).
- a new argument --ignore-error/ignore_error to ignore PathoLogic failed builds (issue 21). With this argument, mpwt will continue to run even if PathoLogic have crashed for some species. It will perform the rest of the workflow for the successful build.
- time measure of each steps of mpwt. They will be printed if you use -v/verbose or they can be accessed at the end of the log_error.txt file (created with --log).

Fix:

- interaction between --clean and the other arguments.
- error if -r/size_reduction is used without output_folder argument.
- a typo error with the name of a function (remove_pgdbs).


Modification:

- split multipwt.py in multiple modules to ease reading (issue 25).
- --clean behaviour when used with -f/input_folder (issue 23) to delete only input species PGDB.
- -r/size_reduction behaviour: it will delete the PGDB from ptools-local and it will move the results into a compressed zip file.
- add table and list in Readme.