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Robaina avatar Robaina commented on August 11, 2024

Idea to make it ultrafast:

seqkit rmdup seq.fasta -s -o filtered.fasta

This command will keep the first duplicated sequence it encounters. Hence, fasta would be first ordered by name, and record names would include a prefix so the one to keep would be sorted before the ones to discard.

To remove sequences also by name and export a file with duplicates:

seqkit infile.fasta -n -s -D duplicates.txt -o outfile.fasta

Seqkit seems to be way more ram-efficient as well...

We could enable keep-sequence selection in preprocess.py as follows:

  1. Locate "keep" sequences first in the merged fasta (e.g. by adding ordered list param to preprocess.py
  2. Update

https://github.com/Robaina/TRAITS/blob/0231882b07d0b76d59873eeca18f3116a328fd2b/code/phyloplacement/database/preprocessing.py#L23-L28

to employ seqkit instead of SeqIO

from metatag.

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