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mckennalab / FlashFry

FlashFry: The rapid CRISPR target site characterization tool
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Discover command help message #9

Closed simone-pignotti closed 5 years ago

simone-pignotti commented 5 years ago

Hi, while for every other command you can get the help message by calling it without arguments, the discover one exits with an error because it tries to open the DB header .header (I guess the default value of the database parameter is the empty string). Should be a very quick fix. Concerning all the help messages, I think it would be useful to include the list of scoring methods and enzymes, even without description, so that one can easily recall the exact parameters without checking the wiki.

Thanks for this awesome tool, it's one of a kind! Simone

aaronmck commented 5 years ago

Totally, I'll add the scoring methods / enzymes to the help messages. I'm traveling until Thursday but should have the fixes for the discover command line option bug in quick. Thanks for the error reporting, it's super helpful.

simone-pignotti commented 5 years ago

No problem, glad that helps!

aaronmck commented 5 years ago

I think both issues above should be fixed in version 1.9.1. I'm also happy to move the scoring descriptions around, for now I put them with the help for -scoringMetrics, but maybe they should go at the top.

simone-pignotti commented 5 years ago

Thanks, the discovery help works now. On the other hand, the -scoringMetrics one includes the output column names, which sometimes differ from the cmd line option (Hsu2013 instead of hsu2013 still works because the match is case insensitive, but Doench2016CFDScore instead of doench2016cfd doesn't).

simone-pignotti commented 5 years ago

Also, in discover the default -flankingSequence is 6, not 10, and the format of -positionOutput is not documented in the wiki (easy to figure out though). Other options that I have tried quickly but I am not sure whether they are working:

But this is going far from the original topic. I can close this once the -scoringMetrics is fixed and open new ones with more details as soon as I have time.

aaronmck commented 5 years ago

Thanks for catching that; I've taken an overdue pass at cleaning out any old command-line args in version 1.9.2. The markExactGenomeHits option was redundant with the current scoring options, so I took that out. The other options listed above are still active. I'll also add some documentation about the output formats in general, which are certainly lacking. Thanks for the heads-up!

simone-pignotti commented 5 years ago

Great, thanks a lot to you!