wenbostar/PDV

Can't parse Tide file

wsnoble opened this issue · 4 comments

wsnoble commented

The documentation says that the database search functionality can parse "MS-GF+, MyriMatch, X!Tandem, OMSSA (convert OMSSA raw result to mzIdentML format using MzidLib: https://github.com/PGB-LIV/mzidlib), Crux, Comet, Mascot, IPeak and
MSFragger." Crux is the name of the toolkit, and it contains two search engines, Tide and Comet. I tried to upload the attached Tide search results file, which ends in .txt. When I do this, the dialog box allows me to specify one of three options: PDV format, MSAmanda and Philosopher. How do I get it to read Tide format? If I select PDV format, then it says the format is not supported.

plasmo-neighbors.trypsin-p.narrow.tide-search.txt

wenbostar commented

For Crux/Tide, we currently support the following formats:

image

We did the test on version 3.2. You can find examples at https://github.com/wenbostar/PDV/blob/master/README.md#database-searching.

wenbostar commented

For comet, we support the following output formats:
image

wsnoble commented

OK, sounds good. Maybe update the documentation to make this clearer?

wenbostar commented

Sorry for the confusion. I have updated the manual to make it clearer.