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BreakerLab / dimpl

DIMPL: Discovery of Intergenic Motifs PipeLine
MIT License
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Database Name in File Name #5

Closed snmalk closed 10 months ago

snmalk commented 4 years ago

I think it'd be helpful to incorporate the database name into the .sto file after Infernal (like before with MultiRavenna). i.e. after running with refseq98, the .sto file would say motifname_refseq98.sto

It'd be easy to tell which file was your output, but also what database was being searched.

kenibrewer commented 4 years ago

@snmalk I think the best way to do this is to:

  1. Create a variable like search_database that gets set in a Jupyter Notebook cell
  2. Pass the variable as an argument to the build_infernal_commands functions
  3. Have build_infernal_commands function copy the search_database variable to the top of the script file for the cluster the same way STEPNAME gets copied.
  4. Rename output files using the new script variable.

Similar to issue #6 this will require changes to the ipynb files, the src/shell/infernal_run_template.sh file and the command_build.py file.

snmalk commented 4 years ago

@kenibrewer Thanks for the input - I was trying a few things and it didn't seem to work, so I'll go about this approach!

kenibrewer commented 10 months ago

Closing issue as stale.