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hallamlab / metapathways2

MetaPathways v2.0: A master-worker model for environmental Pathway/Genome Database construction on grids and clouds
http://hallam.microbiology.ubc.ca/MetaPathways/
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MP not using MetaCyc annotations correctly in *.pf file #61

Closed taltman closed 7 years ago

taltman commented 9 years ago

The PF file creation in MP needs a lot of work. I hope that when some MP devs have some bandwidth, we can work to make better use of them.

One problem is that even despite using the MetaCyc reference database with Blast, the resulting MetaCyc hit is not being added to the correct field in order for PathoLogic to make use of it. There's a 'MetaCyc' attribute in PF files, and if provided with a MetaCyc reaction frame ID, it will assign the ORF directly, with zero ambiguity! Nice!

This should be added, as it will avoid people like me having to go through 50 ORFs in the PathoLogic "Assign Probable Enzyme" dialog manually...

hallamlab commented 7 years ago

as you know, a newer version of MP will soon be released and an alternative ptools input will be available