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lweasel / piquant

A pipeline to assess the quantification of transcripts.

Home Page:http://piquant.readthedocs.org/en/latest/

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Improve naming of parameters.py etc.

lweasel opened this issue · comments

commented

i.e. read sequencing parameters plus the choice of quantification method. At the moment there are too many different things confusingly called "params".

commented

Parameters are no more, everything is now a "piquant option". There are different flavours of option:

  • general piquant options: e.g. the directory into which simulated reads will be written,
  • "quantification run" options: options whose values may be relevant to simulating a set of reads or performing quantification (e.g. the GTF file containing transcript definitions), and
  • "multiple quantification run" options: options taking multiple values, for which reads will be simulated, or quantification performed, for each different value of the option (in combination with each different value of every other such option (e.g. read length, sequence depth, quantification method etc.)

Needs documenting before merging to master. Also the code could do with some tidying, and some tests were lost in the refactor.