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soedinglab / hh-suite

Remote protein homology detection suite.
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3019-7
GNU General Public License v3.0
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addss.pl calls blastpgp and makemat which are legacy blast commands #374

Open Beigephage opened 6 months ago

Beigephage commented 6 months ago

addss.pl runs blastpgp -b 1 -j 1 -h 0.001 -d $dummydb -i $infile -B $tmpfile.in.psi -C $tmpfile.chk 1> $tmpfile.blalog 2> $tmpfile.blalog and &HHPaths::System("$ncbidir/makemat -P $tmpfile"); but both commands are part of legacy blast and not the more recent BLAST+. How do you recommend updating addss.pl to allow this to still run?

Thank you

milot-mirdita commented 6 months ago

We don't intend it update addss.pl currently. I'd be happy to review a pull request though.

Beigephage commented 6 months ago

Hi Milot, how do you suggest running addss.pl without the legacy blast, which is not downloadable? Any help would be appreciated.

Beigephage commented 6 months ago

commented out #"$ncbidir/blastpgp -b 1 -j 1 -h 0.001 -d $dummydb -i $infile -B $tmpfile.in.psi -C $tmpfile.chk 1> $tmpfile.blalog 2> $tmpfile.blalog"

to replace with

"$ncbidir/psiblast -db $dummydb -query $infile -inclusion_ethresh 0.001 -out_pssm $tmpfile.chk -num_iterations 3 -num_alignments 0 1> $tmpfile.blalog 2> $tmpfile.blalog"

and commented out #&HHPaths::System("$ncbidir/makemat -P $tmpfile"); but unfortunately it is still incapable of adding secondary structure to the alignment.