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alternative start codons #48

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cpaight opened this issue Sep 16, 2022 · 1 comment

cpaight commented Sep 16, 2022

Is it possible to set spaln parameters when running ProtHin? I want to specify the translation table I want spaln to use.

Contributor

tomasbruna commented Sep 20, 2022

There is no interface to do this, but you can change them directly in here:

ProtHint/bin/spalnBatch.sh

Lines 60 to 62 in 0385924

    
           "$binDir/../dependencies/spaln" $mode $nonCanonicalFlag -LS -pw -S1 -O1 -l $alignmentLength "$nuc" "$prot" \ 
        
             2> /dev/null | "$binDir/../dependencies/spaln_boundary_scorer" -o "${nuc}_${prot}" -w 10 \ 
        
             -s "$binDir/../dependencies/blosum62.csv" -e $min_exon_score -x $min_exon_score

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