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primer3-org / primer3

Primer3 is a command line tool to select primers for polymerase chain reaction (PCR).
GNU General Public License v2.0
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Batching multiple sequences in ntthal #12

Closed nh13 closed 5 years ago

nh13 commented 6 years ago

I was wondering the appetite for a PR where we could batch many sequences to run ntthal. I want to perform 100K+ invocations of ntthal, and I'd rather just send ntthal a stream of data and have one ntthal process handle all the requests. I am only modifying the sequences I pass in (-s1 and -s2) so I see a few options:

  1. If -s1 and -s2 are not defined, then ntthal reads in from standard input.
  2. A new argument (-f?) that specifies a file with input sequences to process.

Thanks for considering this idea!

bioinfo-ut commented 5 years ago

Thank you for the idea, but this enhancement is probably not our first priority. This should be relatively easy to achieve with the help of a small bash or PERL script. With 100K primer pairs you have to post-process the output with the help of some script anyway.

nh13 commented 5 years ago

Unfortunately, I do have a script and it still takes too long to run the utility 100K+ times. My question was if you’d accept a PR (from me) not that you’d have to write it. My apologies if that wasn’t clear.

bioinfo-ut commented 5 years ago

Feel free to open pull request, if thats what you meant by "appetite for a PR". It was not clear indeed :-).