SearchCLI: MS-GF+ options

compomics / searchgui

Highly adaptable common interface for proteomics search and de novo engines

http://compomics.github.io/projects/searchgui.html

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SearchCLI: MS-GF+ options #332

Closed tivdnbos closed 1 year ago

tivdnbos commented 1 year ago

Hi,

I was wondering how I could define the following options in the SearchCLI search with MS-GF+:

I would like to turn the MSGF+ addFeatures option to 1 (default 0); in SearchGUI this can be found under MS-GF+ Advanced Settings > additional output
I have a target/decoy generic database with "decoy_" prefix as decoy-tag. How can I specify this in the SearchCLI? In SearchGUI, this can be defined in the "Edit fasta parsing" options.

Best, Tim

hbarsnes commented 1 year ago

Hi Tim,

The parameters can all be set via https://github.com/compomics/compomics-utilities/wiki/IdentificationParametersCLI.

For the specific MS-GF+ parameters please see: https://github.com/compomics/compomics-utilities/wiki/IdentificationParametersCLI#ms-gf-advanced-parameters. The one you are looking for seems to be -msgf_additional 1.

The database processing options are set in the same way and the parameters are listed here: https://github.com/compomics/compomics-utilities/wiki/IdentificationParametersCLI#database-processing.

The generated parameter file can then be used as input to the SearchCLI command line.

Best regards, Harald

tivdnbos commented 1 year ago

Thanks Harald!

tivdnbos commented 1 year ago

Hi Harald,

Sorry to re-open this again. Currently, the analysis works correctly, but the name of my output files isn't. I iterate over different fasta files to search one mgf file with the different databases, and use as -output_default_name the name of the fasta file (minus the .fasta extension). When I echo this command in bash, it looks correct; however msgf+ uses the name of the mgf. When I remove the -output_default_name option, I would expect searchgui_out, but it stays the mgf file name.

Might this be a bug?

Best, Tim

hbarsnes commented 1 year ago

Hi Tim,

The -output_default_name option only controls the name of the zipped (combined) export from SearchGUI and not the names of the individual search results files from the different search engines. For MS-GF+ the search results file will always be named "spectrum file name without extension" + ".msgf.mzid".

Best regards, Harald

tivdnbos commented 1 year ago

Oooh, okay, I'll work around that then :)

Thanks Harald!