mpwt 0.5.3

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.

mpwt 0.5.2

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).

mpwt 0.5.1

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.

mpwt 0.5

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.

mpwt 0.4.2.4

Fix:

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

mpwt 0.4.2.3

Fix:

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

mpwt 0.4.2.2

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.

mpwt 0.4.2.1

Fix:

• error with outdated argument in cleaning_input.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

mpwt 0.4.2

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.

mpwt 0.4.1

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.