Clarify filename requirements for --primerTarget (disallow hyphens)#18
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couunderbarz wants to merge 1 commit into
Open
Clarify filename requirements for --primerTarget (disallow hyphens)#18couunderbarz wants to merge 1 commit into
couunderbarz wants to merge 1 commit into
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This pull request updates the documentation for the
--primerTargetoption to explicitly state that input filenames must not contain hyphens (-).I encountered issues when using filenames such as
Ecoli-1_cds.fna, which led to incorrect behavior during downstream processing—specifically, the number of unique genes inUniqueGenesPlot.pdfwas miscounted.This appears to be caused by how filenames are parsed using
split('-')(e.g., https://github.com/Tropini-lab/PUPpy/blob/main/scripts/puppy-primers#L792C46-L792C58 ), where hyphens in the unique identifier part result in unexpected splitting.To prevent confusion and misbehavior, this PR clarifies the filename constraints in the CLI help and/or documentation.