fixed a bug related to the TM coloring output

cbcrg · Dec 9, 2015 · 1ebfcc7 · 1ebfcc7
1 parent 3628a4c
commit 1ebfcc7
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Showing 4 changed files with 15 additions and 5 deletions.
diff --git a/lib/perl/lib/filters/fasta_seq2hmmtop_fasta.pl b/lib/perl/lib/filters/fasta_seq2hmmtop_fasta.pl
@@ -47,11 +47,12 @@
 
 if ($mode eq "hmmtop")
   {
+
     check_configuration ("hmmtop");
     if (-e $arch){$ENV{'HMMTOP_ARCH'}=$arch;}
     elsif (-e $ENV{HMMTOP_ARCH}){$arch=$ENV{HMMTOP_ARCH};}
     elsif (-e "$MCOFFEE/hmmtop.arch"){$arch=$ENV{'HMMTOP_ARCH'}="$MCOFFEE/hmmtop.arch";}
-    elsif (-e "$hmmtop_home/hmmtop.arc"){$arch=$ENV{'HMMTOP_ARCH'}="$hmmtop_home/hmmtop.arc";}
+    elsif (-e "$hmmtop_home/hmmtop.arch"){$arch=$ENV{'HMMTOP_ARCH'}="$hmmtop_home/hmmtop.arch";}
     else {myexit(flush_error ( "Could not find ARCH file for hmmtop"));}
 
 
@@ -60,6 +61,7 @@
     elsif (-e "$MCOFFEE/hmmtop.psv"){$psv=$ENV{'HMMTOP_PSV'}="$MCOFFEE/hmmtop.psv";}
     elsif (-e "$hmmtop_home/hmmtop.psv"){$psv=$ENV{'HMMTOP_PSV'}="$hmmtop_home/hmmtop.psv";}
     else {myexit(flush_error ( "Could not find PSV file for hmmtop"));}
+
   }
 elsif ($mode eq "gor")
   {
@@ -98,12 +100,13 @@
 %seq=read_fasta_seq($fmsq2);
 %seq=fasta2sample(\%seq, $sample);
 
-if (1==2 && $mode eq "hmmtop" && $output eq "cons")
+if (1==2 &&$mode eq "hmmtop" && $output eq "cons")
   {
     fasta2hmmtop_cons($outfile,\%seq);
   }
 else
   {
+
     %pred=fasta2pred(\%seq, $mode);
     %predA=pred2aln (\%pred, \%seq);
 
@@ -196,7 +199,13 @@ sub fasta2hmmtop_pred
 
 
     output_fasta_seq (\%seq,$tmp_in, "seq");
+
+
     `hmmtop -if=$tmp_in -sf=FAS -pl 2>/dev/null >$tmp_out`;
+
+
+
+
     open ($o, ">$tmp");
     open ($i, "$tmp_out");
     while (<$i>)

diff --git a/lib/perl/lib/scripts/tc_generic_method.pl b/lib/perl/lib/scripts/tc_generic_method.pl
@@ -169,7 +169,7 @@
   }
 elsif ( $mode eq "tm_template")
   {
-    &seq2tm_template ($mode, "", &my_get_opt ( $cl, "-infile=",1,1,"-arch=",1,1,"-psv=",1,1, "-outfile=",1,0));
+    &seq2tm_template ($mode,&my_get_opt ( $cl, "-infile=",1,1,"-arch=",1,1,"-psv=",1,1, "-outfile=",1,0));
   }
 elsif ( $mode eq "psitm_template")
   {

diff --git a/lib/util_lib/aln_convertion_util.c b/lib/util_lib/aln_convertion_util.c
@@ -5849,10 +5849,11 @@ Sequence * seq2template_seq ( Sequence *S, char *template_list, Fname *F)
     }
   else if ( strm ( template_list, "TM"))
     {
-
+      
       /*predict transmembrane structure*/
       check_program_is_installed (HMMTOP_4_TCOFFEE,NULL, NULL,HMMTOP_ADDRESS, INSTALL_OR_DIE);
       sprintf ( buf, "SCRIPT_tc_generic_method.pl@mode#tm_template@arch#%s/%s@psv#%s/%s@type#_T_",get_mcoffee_4_tcoffee(), "hmmtop.arch", get_mcoffee_4_tcoffee(), "hmmtop.psv");
+
       S=seq2template_seq (S,buf, F);
       return S;
     }

diff --git a/lib/util_lib/reformat.c b/lib/util_lib/reformat.c
@@ -2616,7 +2616,7 @@ int main_output  (Sequence_data_struc *D1, Sequence_data_struc *D2, Sequence_dat
 
 	    if (!ns)
 	      {
-		add_warning ( stderr, "Cannot output tm_html:_E_ template file (sec. struc.) is required for this output ", PROGRAM);
+		add_warning ( stderr, "Cannot output sec_html:_E_ template file (sec. struc.) is required for this output ", PROGRAM);
 	      }
 	    output_color_html  ( A, ST, out_file);
 	  }