"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);
