New version of exonerate (0.7.1). Path to executable updated (may be

overridden by command line options or configuration file) and
environment variables removed (since the old valus are now the default
values of exonerate anyway).

misc-scripts/protein_match/exonerate_wrapper.pl

@@ -4,7 +4,7 @@ use strict;
 use warnings;
 use diagnostics;
 
-use Data::Dumper;
+#use Data::Dumper;
 use Getopt::Std;
 use IO::Handle;
 
@@ -31,7 +31,7 @@ use IO::Handle;
 # 7	Alignment start in query	integer
 # 8	Alignment end in query		integer
 # 9	Score				integer
-# 10	Cigar line			string
+# 10	Cigar line (Ensembl style)	string
 #
 #----------------------------------------------------------------------
 #
@@ -56,7 +56,7 @@ use IO::Handle;
 
 my $q_fa='/acari/work4/mongin/anopheles_mai/mapping/Primary/peptides_new.fa';
 my $t_fa='/acari/work4/mongin/anopheles_mai/mapping/Primary/total.fa';
-my $e_cmd='/acari/work2/gs2/gs2/local/OSF1/bin/exonerate';
+my $e_cmd='/usr/local/ensembl/bin/exonerate-0.7.1';
 my $q_min=25;
 my $t_min=25;
 my $s_min=99;
@@ -177,16 +177,12 @@ if (defined($fin) && length($fin) != 0 &&
 # Set default options for exonerate using environment variables (may be
 # overridden by command line options).
 $ENV{EXONERATE_EXONERATE_FSMMEMORY}      = 512;
-$ENV{EXONERATE_EXONERATE_HSPDROPOFF}     = 5;
-$ENV{EXONERATE_EXONERATE_HSPTHRESHOLD}   = 30;
 $ENV{EXONERATE_EXONERATE_MODEL}          = 'affine:local';
-$ENV{EXONERATE_EXONERATE_PROTEINWORDLEN} = 6;
-$ENV{EXONERATE_EXONERATE_WORDTHRESHOLD}  = 3;
 
 my $e_ryo =
     '%qi\\\t%qal\\\t%ql\\\t%qab\\\t%qae\\\t' .
     '%ti\\\t%tal\\\t%tl\\\t%tab\\\t%tae\\\t' .
-    '%p\\\t%s\\\t%C\\\n';
+    '%pi\\\t%s\\\t%C\\\n';
 
 my $e_opt =
     "--showalignment no --showvulgar no -q $q_fa -t $t_fa --ryo $e_ryo " .