undocumented beta release tested with beta tests

cbcrg · Dec 2, 2020 · 708f8d5 · 708f8d5
1 parent ebcc05e
commit 708f8d5
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diff --git a/binaries/macosx/t_coffee b/binaries/macosx/t_coffee
diff --git a/build/web-readme.txt b/build/web-readme.txt
@@ -1,6 +1,6 @@
 T-Coffee distribution 
 =====================
-Version_13.45.28.96a2885 #_#UPDATE_VERSION -- Populated by edit_version.pl
+Version_13.45.29.ebcc05e #_#UPDATE_VERSION -- Populated by edit_version.pl
 The version ID is organized as follows: <Major Release>.<Latest Stable>.<Latest Beta>.<Github version tag>
 Content of this directory: 
 Linux Installation:

diff --git a/docs/.html/.buildinfo b/docs/.html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 985c45032412ae09b52cd20e7d8a6d23
+config: 889835bb5ded7a69ce3c6de9b88e055b
 tags: 33eac41acc08762151beb8f3b7b86c8f
diff --git a/docs/.html/.doctrees/environment.pickle b/docs/.html/.doctrees/environment.pickle
diff --git a/docs/.html/_static/documentation_options.js b/docs/.html/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: 'Version_13.45.28.96a2885',
+    VERSION: 'Version_13.45.29.ebcc05e',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     FILE_SUFFIX: '.html',

diff --git a/docs/.html/index.html b/docs/.html/index.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>T-Coffee Version_13.45.28.96a2885 documentation</title>
+  <title>T-Coffee Version_13.45.29.ebcc05e documentation</title>
 
 
 
@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                Version_13.45.28.96a2885
+                Version_13.45.29.ebcc05e
               </div>
 
 
@@ -716,7 +716,7 @@
 
       <li><a href="index.html#document-index">Docs</a> &raquo;</li>
 
-      <li>T-Coffee Version_13.45.28.96a2885 documentation</li>
+      <li>T-Coffee Version_13.45.29.ebcc05e documentation</li>
 
 
       <li class="wy-breadcrumbs-aside">

diff --git a/docs/.html/objects.inv b/docs/.html/objects.inv
diff --git a/docs/conf.py b/docs/conf.py
@@ -54,9 +54,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'Version_13.45.28.96a2885' #_#UPDATE_VERSION_TAG1 -- Populated by edit_version.pl
+version = u'Version_13.45.29.ebcc05e' #_#UPDATE_VERSION_TAG1 -- Populated by edit_version.pl
 # The full version, including alpha/beta/rc tags.
-release = u'Version_13.45.28.96a2885' #_#UPDATE_VERSION_TAG2 -- Populated by edit_version.pl
+release = u'Version_13.45.29.ebcc05e' #_#UPDATE_VERSION_TAG2 -- Populated by edit_version.pl
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/lib/dp_lib/phylo3d.c b/lib/dp_lib/phylo3d.c
@@ -160,7 +160,9 @@ Alignment *phylo3d_gt (Alignment *inA, Constraint_list *CL)
   for (n=0,s1=0; s1<A->nseq-1; s1++)
     {
       int rs1, rs2;
-      rs1=name_is_in_hlist (A->name[s1], S->name, S->nseq);
+      int cls1, cls2;
+      cls1=name_is_in_hlist (A->name[s1], (CL->S)->name, (CL->S)->nseq);
+      rs1 =name_is_in_hlist (A->name[s1],      S->name,        S->nseq);
       for ( s2=s1+1; s2<A->nseq; s2++, n++)
 	{
 	  int  *buf_pos_s1, *buf_pos_s2;
@@ -169,9 +171,12 @@ Alignment *phylo3d_gt (Alignment *inA, Constraint_list *CL)
 	  rs2=name_is_in_hlist (A->name[s2], S->name, S->nseq); 
 
 	  if (!align_method)B=align_two_sequences (S->seq[s1], S->seq[s2], "blosum62mt", -8, -1, "myers_miller_pair_wise");
-	  else B=align_two_structures  (CL->S, rs1, rs2,align_method);
-
-
+	  else 
+	    {
+	      cls2=name_is_in_hlist (A->name[s2], (CL->S)->name, (CL->S)->nseq);
+	      B=align_two_structures  (CL->S, cls1, cls2,align_method);
+	    }
+
 
 	  pos=aln2pos_simple(B,2);
 	  msa2column_list (B,D->colrep);

diff --git a/lib/io_lib/tree_util.c b/lib/io_lib/tree_util.c
@@ -8399,7 +8399,7 @@ Alignment * sorttrim (Alignment *A,int ntrim)
   newn=0;
   while ( newn<maxnseq && newn<ntrim)
     {
-      for (bin=0; bin<nbin; bin++)
+      for (bin=0; bin<nbin && newn<ntrim; bin++)
 	{
 	  if (used[bin]==max[bin])continue;
 	  else s=lu[bin][used[bin]++];

diff --git a/lib/perl/lib/scripts/mmseqs2prf.pl b/lib/perl/lib/scripts/mmseqs2prf.pl
@@ -66,7 +66,7 @@
     elsif ($ARGV[$a] eq "-s")            {$S="-s ".$ARGV[++$a];}
 
   }
-if (!$dbf || !-e $dbf){print STDERR "ERROR: mmseqs2prf required a database via -protein_db $FATAL\n";exit ($EXIT_FAILURE);}
+if (!$dbf){print STDERR "ERROR: mmseqs2prf required a database via -protein_db $FATAL\n";exit ($EXIT_FAILURE);}
 if (!$qff){print STDERR "ERROR: mmseqs2prf required a query    -q $FATAL";exit ($EXIT_FAILURE);}
 if (!is_installed("mmseqs")){print STDERR "ERROR: mmseqs2prf required mmseqs to be installed $FATAL\n";exit ($EXIT_FAILURE);}
 
@@ -90,6 +90,8 @@
     $q{search }="$cacheq/out.MMSEQSSEARCH";
     $q{convert}="$cacheq/out.MMSEQSCONVERT";
 
+
+
     if (!-e $q{search} || $FORCE)
       {system ("mmseqs search $q{db} $db{db} $q{search} $db{index} $S -a $QUIET");}
     else{print STDERR "! mmseqs search : use cached $q{search}\n";}
@@ -101,7 +103,8 @@
 else
   {
      $q{convert}="$cacheq/out.MMSEQSCONVERT";
-     split_mmseqs($qf, $cacheq, $updateq, $
+     split_mmseqs($qf, $cacheq, $updateq, $dbf, $cachedb, $updatedb,$S,$q{convert});
+   }
 
 mmseqs2prf ($q{convert},$outdir,$prot_min_sim,$prot_max_sim, $prot_min_cov,%H);
 prf2trimprf($outdir,$psitrim_mode, $psitrim_tree, $psitrim, %H);
@@ -168,8 +171,89 @@ sub h2lu
       }
     return %lu;
   }
-
 sub mmseqs2prf
+  {
+    #"query[0],target[1],qaln[2],taln[3],qstart[4],qend[5],pident[6],qcov[7],qlen[8]\" $QUIET");
+    my ($out,$outdir,$min_id, $max_id,$min_cov, %h)=@_;
+    my $ff  =new FileHandle;
+    my $prf =new FileHandle;
+    my $nn;
+    my $tot;
+    my $psn;
+    my %lu=h2lu(%h);
+    my %luf;
+
+    open ($ff,$out);
+    while (<$ff>)
+      {
+	my $l=$_;
+	my @ll=split (/\s/, $l);
+	my $sn=$ll[0];
+	my $f =$lu{$sn}{0};
+	my $cf=$h {$f}{prf}{$sn}{absolute};
+
+	if ($sn ne $psn)
+	  {
+	    close $prf;
+	    if ($luf{$cf}){open ($prf, ">>$cf");}
+	    else
+	      {		
+		open ($prf, ">$cf");
+		print $prf ">$sn\n$h{$f}{seq}{$sn}\n";
+	      }
+	  }
+	$nn=++$luf{$cf};
+	$psn=$sn;
+
+	my $id=$ll[6]*100;
+	my $cov=$ll[7]*100;
+	my $len=$ll[8];
+
+	if ($id<=$max_id && $id>=$min_id && $cov>$min_cov)
+	  {
+	    print $prf ">$sn\_$nn\n";
+	    for (my $a=1; $a<$ll[4]; $a++){print $prf "-"}
+
+	    my @ql=split (//,$ll[2]);
+	    my @tl=split (//,$ll[3]);
+	    my $qlen=length($ll[2]);
+	    for (my $a=0; $a<$qlen; $a++)
+	      {
+		if ($ql[$a] ne "-"){print $prf "$tl[$a]";}
+	      }
+	    for (my $a=$ll[5]; $a<$len; $a++){print $prf "-"}
+	    print $prf "\n";
+	  }
+      }
+    close($prf);
+    close($ff);
+
+    # checkout the un-used ones
+    foreach my $sn (keys(%lu))
+      {
+	my $f=$lu{$sn}{0};
+
+	if (!-e $h{$f}{prf}{$sn}{absolute})
+	  {
+	    open ($prf,">$h{$f}{prf}{$sn}{absolute}");
+	    print $prf ">$sn\n$h{$f}{seq}{$sn}\n";
+	    close (prf);
+	  }
+      }
+    #duplicate prf files that are shared by different input datasets
+    foreach my $sn (keys (%lu))
+      {
+	my $f0=$lu{$sn}{0};
+
+	foreach my $i (keys(%{$lu{$sn}}))
+	  {	
+	    my $f=$lu{$sn}{$i};
+	    if (! -e $h{$f}{prf}{$sn}{absolute}){system ("cp $h{$f0}{prf}{$sn}{absolute} $h{$f}{prf}{$sn}{absolute}");}
+	  }
+      }
+  }
+
+sub mmseqs2prf_old
   {
     #"query[0],target[1],qaln[2],taln[3],qstart[4],qend[5],pident[6],qcov[7],qlen[8]\" $QUIET");
     my ($out,$outdir,$min_id, $max_id,$min_cov, %h)=@_;
@@ -579,14 +663,17 @@ sub split_mmseqs
       my ($qf,$cacheq,$updateq, $db,$cachedb, $updatedb, $s,$out)=@_;
       my @dbl=string2fasta_list($db);
 
+      print "OUT=$out\n";
+
       foreach my $d (@dbl)
 	{
-	  my %db=file2db($dbf,$cachedb, $updatedb);
-	  my %q =file2db($qf, $cacheq , $updateq);
-
-	  $q{search }="$cacheq/$d.MMSEQSSEARCH";
-	  $q{convert}="$cacheq/$d.MMSEQSCONVERT";
-
+	  print "! Process Database $d\n";
+	  my %db=file2db($d ,$cachedb,$updatedb);
+	  my %q =file2db($qf,$cacheq ,$updateq);
+	  my $ld=abs2file ($d);
+	  $q{search }="$cacheq/$ld.MMSEQSSEARCH";
+	  $q{convert}="$cacheq/$ld.MMSEQSCONVERT";
+
 	  system ("mmseqs search $q{db} $db{db} $q{search} $db{index} $s -a $QUIET");
 	  system ("mmseqs convertalis $q{db} $db{db} $q{search} $q{convert} --format-output \"query,target,qaln,taln,qstart,qend,pident,qcov,qlen\" $QUIET");
 	  system ("cat $q{convert} >> $out");

diff --git a/lib/version/build_version.version b/lib/version/build_version.version
@@ -1 +1 @@
-28
+29
diff --git a/lib/version/github.version b/lib/version/github.version
@@ -1 +1 @@
-* master 96a2885 undocumented beta release tested with beta tests
+* master ebcc05e undocumented beta release tested with beta tests
diff --git a/lib/version/version_number.version b/lib/version/version_number.version
@@ -1 +1 @@
-Version_13.45.28.96a2885
+Version_13.45.29.ebcc05e