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Avoid length limit for input fasta ids

Open alpae opened this issue 7 months ago • 1 comments

The enforced length limit on the fasta IDs is annoying.

https://github.com/DessimozLab/FastOMA/blob/38b299167435f16c781dfe065d96e184d6decf8d/FastOMA/check_input.py#L50

we could replace all the IDs with a lookup table. however, there are a few things to consider:

  • doing it before OMAmer mapping means the results cannot easily be reused / existing omamer placements are invalid.
  • debugging will involve an extra (mental) mapping step.
  • generally requires all reporting steps to replace the mapping again.

One option could be to store the mapping in a sqlite database. comments wellcome.

alpae avatar Jul 24 '24 12:07 alpae