bigbio
Does not add second enzyme to Comet search
Description of the bug
My SDRF file has two digestion enzymes (two columns comment[cleavage agent details]). But only one is input in CometAdapter. Implement a --second_enzyme that will take the second one maybe? Is it Sdrf_parser problem?
Command used and terminal output
Relevant files
No response
System information
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Yes, MSGFAdapter and SageAdapter don't support multiple enzymes either, right? @timosachsenberg @ypriverol
They don't. Actually @MetteBoge if you use Trypsin + Lysc we normally use only Trypsin. We don't support yet multiple enzymes. See issue #79
I had both columns in the sdrf file but only lys-c was parsed into comet adapter. I just read that comet adapter has --second_enzyme option. Is there a reason why it is not supported?
And does this mean there is no reason to add cleavage agent details in the sdrf file?
What we are doing in this case is to add the major enzyme basically Trypsin only for now until the pipeline supports multiple enzymes. Then only leave in the SDRF Trypsin,.
@ypriverol I think until we support passing through multiple enzymes, the SDRF parser should combine the enzymes from the SDRF, print a warning and pass only Trypsin to downstream tools. Otherwise, all the datasets get annotated wrongly just because multiple enzymes are not supported.
Actually this is a great idea, @fabianegli or @daichengxin can you update sdrf-pipelines with this feature.