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Replace PHMM filtering code #20

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jackscanlan opened this issue Oct 16, 2024 · 2 comments
Open

Replace PHMM filtering code #20

jackscanlan opened this issue Oct 16, 2024 · 2 comments
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@jackscanlan
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Investigate if HMMER3 is better or faster
@jackscanlan
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If using hmmer3, use the hmmsearch command and then parse the --tblout output using code reimplemented from rhmmer: https://github.com/arendsee/rhmmer/blob/master/R/parse.R

jackscanlan pushed a commit that referenced this issue Nov 19, 2024
stop codon filtering now uses correct genetic code for each sequence …
de602aa 
…based on taxonomy; filtering code replaced to now check if any reading frames are stop codon free; related to #20
@jackscanlan
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de602aa actually doesn't relate to this

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