[med-svn] [Git][med-team/t-coffee][master] Extended path by Aaron M. Ucko

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / t-coffee


Commits:
337171d8 by Andreas Tille at 2020-04-20T21:02:31+02:00
Extended path by Aaron M. Ucko

- - - - -


1 changed file:

- debian/patches/bypass_legacy_blast.patch


Changes:

=====================================
debian/patches/bypass_legacy_blast.patch
=====================================
@@ -5,6 +5,15 @@ Description: See origin
 
 --- 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;}
@@ -14,6 +23,15 @@ Description: See origin
  	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;
  	    }
@@ -47,3 +65,21 @@ Description: See origin
  	      }
  	    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);



View it on GitLab: https://salsa.debian.org/med-team/t-coffee/-/commit/337171d82d9a63fb0ccd09b809ef743e72becd07

-- 
View it on GitLab: https://salsa.debian.org/med-team/t-coffee/-/commit/337171d82d9a63fb0ccd09b809ef743e72becd07
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