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GFF3 annotation filtering

Hi, Is there a GFF3 annotation filtering tool:

  • which removes genes without a description and writes those in a different file
  • which removes gene names specific to user input and writes those in a different file?

Thank you in advance,

gene genome
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updated by Buffo Buffo • written by Ric Ric

Firstly, (as a side note ;) ) I would personally try to avoid adding gene description etc in a GFF file format. iI's not meant to hold that kind of info

Secondly, is the GFF file "complex"? if not then perhaps using linux commands such as awk or grep will get the job done?

• 0 views • link
written by lieven.sterck lieven.sterck

1 answer

You can use GFFExaminer from Biopython.

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written by Buffo Buffo

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