Thanks again. Applied an pushed. Please feel free to directly commit to Git. I don't see any advantage to communicate via BTW. :-)
Kind regards, Andreas. On Mon, Apr 20, 2020 at 01:06:42PM -0400, Aaron M. Ucko wrote: > "Aaron M. Ucko" <[email protected]> writes: > > > I've attached a full patch. > > Extended to cover calls to blastall, which is also a legacy entry point. > (I left blast_msa_old's call as is, since it's untranslatable without > the crucial -p argument, and nothing calls that subroutine anyway.) > > -- > Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org) > http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/[email protected] > > --- a/example/tc_generic_method.pl > +++ b/example/tc_generic_method.pl > @@ -688,7 +688,7 @@ sub blast_msa > > > #&safe_system ("formatdb -i $db"); > - if ($blast eq "blastp"){&safe_system ("blastall -i $infile -d $db -m7 > -p blastp -o io");} > + if ($blast eq "blastp"){&safe_system ("blastp -db $db -query $infile > -out io -outfmt 5 -seg yes");} > elsif ($blast eq "blastn"){&safe_system ("blastn -query $infile -db $db > -outfmt 5 -word_size 4 -out io");} > > &set_blast_type ("io"); > @@ -1183,7 +1183,7 @@ sub pg_is_installed > if ($r eq ""){$r=0;} > else {$r=1;} > > - if ($r==0 && is_blast_package ($p)){return pg_is_installed > ("legacy_blast.pl");} > + if ($r==0 && is_blast_package ($p)){return pg_is_installed ("blastn");} > else {return $r;} > } > } > @@ -2597,7 +2597,7 @@ sub run_blast > &check_configuration ("blastall"); > if ($method eq "blastp") > { > - $command="blastall -d $db -i $infile -o $outfile -m7 -p blastp"; > + $command="blastp -db $db -query $infile -out $outfile -outfmt 5 > -seg yes"; > } > &safe_system ($command); > } > @@ -2611,26 +2611,20 @@ sub run_blast > $cl_db=$db; > } > > - ## > ## BLAST+ provide different binaries names and CLI options > - ## Use the 'legacy_blast.pl' to keep compatibility with old > blast commands > - ## > - $path=`which legacy_blast.pl 2>/dev/null`; > - $path=`dirname $path`; > - chomp($path); > if ($method eq "blastp"){ > - &check_configuration("legacy_blast.pl"); > - $command="legacy_blast.pl blastpgp --path $path -d > $cl_db -i $infile -o $outfile -m7 -j1"; > + &check_configuration("psiblast"); > + $command="psiblast -db $cl_db -query $infile > -num_iterations 1 -out $outfile -outfmt 5"; > } > elsif ($method eq "psiblast") > { > - &check_configuration("legacy_blast.pl"); > - $command="legacy_blast.pl blastpgp --path $path -d $cl_db -i > $infile -o $outfile -m7 -j5"; > + &check_configuration("psiblast"); > + $command="psiblast -db $cl_db -query $infile -num_iterations 5 > -out $outfile -outfmt 5"; > } > elsif ($method eq "blastn") > { > - &check_configuration("legacy_blast.pl"); > - $command="legacy_blast.pl blastall --path $path -p blastn -d > $cl_db -i $infile -o $outfile -m7 -W6"; > + &check_configuration("blastn"); > + $command="blastn -task blastn -db $cl_db -query $infile > -word_size 6 -out $outfile -outfmt 5"; > } > print "$command\n"; > &safe_system ($command); > @@ -2859,7 +2853,7 @@ sub seq2tblastx_lib > } > close (F); > &safe_system ("formatdb -i infile -p F"); > - &safe_system ("blastall -p tblastx -i infile -d infile -m 7 > -S1>blast.output"); > + &safe_system ("tblastx -db infile -query infile -out blast.output > -outfmt 5"); > > ncbi_tblastx_xml2lib_file ("outfile", file2string ("blast.output")); > &set_temporary_dir ("unset",$mode, $method, "outfile",$outfile); > @@ -2890,7 +2884,7 @@ sub seq2tblastpx_lib > close (F); > &safe_system("t_coffee -other_pg seq_reformat -in infile -output > tblastx_db1 > tblastxdb"); > &safe_system ("formatdb -i tblastxdb -p T"); > - &safe_system ("blastall -p blastp -i tblastxdb -d tblastxdb -m7 > >blast.output"); > + &safe_system ("blastp -db tblastxdb -query tblastxdb -out blast.output > -outfmt 5"); > ncbi_tblastpx_xml2lib_file ("outfile", file2string ("blast.output"), %s); > &set_temporary_dir ("unset",$mode, $method, "outfile",$outfile); > myexit ($EXIT_SUCCESS); -- http://fam-tille.de
