"Aaron M. Ucko" <u...@debian.org> 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/?a...@monk.mit.edu
--- 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);