[Debian-med-packaging] Bug#956850: Bug#956848: ncbi-blast+-legacy: Please provide /usr/bin/blastpgp.pl (including .pl extension)

[Andreas Tille]

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" <ucko at 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/?amu@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);


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