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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