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grunwaldlab / effectR

An R package to call oomycete effectors
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Regarding regex pattern #20

Closed Ramakrishna0007 closed 3 years ago

Ramakrishna0007 commented 5 years ago

good evening sir... this is Ramakrishna. "^\w{10,40}\w{1,96}R\wLR\w{1,40}eer" this regex pattern is searching for proteins {1,96}R\wLR == only having RXLR motifs separately and {1,40}eer == having EER motifs separately..

Sir, actually I need a pattern search for proteins having only "^\w{10,40}\w{1,96}R\wLR\w{1,40}eer" this pattern and not separately, i don't want only RXLR and only EER having proteins. I tried with subsetting complete motifs form data frame, even though I am getting proteins with only RXLR and only EER and both.

Tabima commented 5 years ago

Hi, I don't seem to understand your question, sorry.

You want only the proteins with both RxLR and EER proteins? If so then run the pipeline, and at the effector.summary step select only the proteins that show "Complete" in the motif table.