undocumented beta release tested with beta tests

build/web-readme.txt

@@ -1,6 +1,6 @@
 T-Coffee distribution 
 =====================
-Version_13.45.19.70f594b #_#UPDATE_VERSION -- Populated by edit_version.pl
+Version_13.45.20.8ffe5eb #_#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:

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: 08afd6aa575ff1431e8c3ff4b39ee8ad
+config: 25666fbeda4a1ae6820dd19181a9f1b7
 tags: 33eac41acc08762151beb8f3b7b86c8f

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_13.45.19.70f594b',
+    VERSION: 'Version_13.45.20.8ffe5eb',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     FILE_SUFFIX: '.html',

docs/.html/index.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>T-Coffee Version_13.45.19.70f594b documentation</title>
+  <title>T-Coffee Version_13.45.20.8ffe5eb documentation</title>
 
 
 
@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                Version_13.45.19.70f594b
+                Version_13.45.20.8ffe5eb
               </div>
 
 
@@ -716,7 +716,7 @@
 
       <li><a href="index.html#document-index">Docs</a> &raquo;</li>
 
-      <li>T-Coffee Version_13.45.19.70f594b documentation</li>
+      <li>T-Coffee Version_13.45.20.8ffe5eb documentation</li>
 
 
       <li class="wy-breadcrumbs-aside">

docs/conf.py

@@ -54,9 +54,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'Version_13.45.19.70f594b' #_#UPDATE_VERSION_TAG1 -- Populated by edit_version.pl
+version = u'Version_13.45.20.8ffe5eb' #_#UPDATE_VERSION_TAG1 -- Populated by edit_version.pl
 # The full version, including alpha/beta/rc tags.
-release = u'Version_13.45.19.70f594b' #_#UPDATE_VERSION_TAG2 -- Populated by edit_version.pl
+release = u'Version_13.45.20.8ffe5eb' #_#UPDATE_VERSION_TAG2 -- Populated by edit_version.pl
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

lib/dp_lib/phylo3d.c

@@ -208,7 +208,7 @@ int free_3dD (p3D*D)
 
 p3D* fill_p3D (Alignment *A, Constraint_list *CL)
 {
-  int a;
+  int a,b;
   p3D *D=(p3D*)vcalloc ( sizeof (p3D), 1);
   D->A=A;
   D->CL=CL;
@@ -240,6 +240,8 @@ p3D* fill_p3D (Alignment *A, Constraint_list *CL)
 
 
   D->pos=aln2pos_simple (A, A->nseq);
+
+
   D->dm3d=aln2dm3d (A, CL, &D->extremed);
   if (getenv ("maxd_4_TCOFFEE"))
     {
@@ -395,8 +397,8 @@ int filter_columns_with_dist_strict(Alignment *B, int **pos,int **col, int***dm,
 	  int r1=pos[s][c1]-1;
 	  int r2=pos[s][c2]-1;
 	  if (r1<r2){int rb=r1; r1=r2;r2=rb;}
-
-	  if (r1>=0 && r2>=0 && dm[s][r1-1][r2-1]<=maxd)count++;
+	  	  
+	  if (r1>=0 && r2>=0 && dm[s][r1][r2]<=maxd)count++;
 	}
       if ( count==B->nseq)
 	{
@@ -657,8 +659,7 @@ double pair2dist(p3D *D, int s1, int s2)
       if (D->used_site_pair)D->used_site_pair[c1][c2]=D->used_site_pair[c2][c1]=1;
 
     }
-
-  if (max<MY_EPSILON)score=-100;
+    if (max<MY_EPSILON)score=-100;
   else score=(double)100*((double)1 - (score/max));
   return score;
 }

lib/io_lib/tree_util.c

@@ -8354,8 +8354,70 @@ int ktree2klist (KT_node K, KT_node *KL, int *n)
   return n[0];
 }
 
+Alignment * sorttrim (Alignment *A,int ntrim)
+{
+  int **lu, *max, *used;
+  int s, c;
+  FILE *fp;
+  char *tmp=vtmpnam (NULL);
+  int maxnseq;
+  int newn;
+  int bin,nbin=100;
+  if (!A) return A;
+  else if (A->nseq<=ntrim)return A;
+
+
+
+
+  lu=declare_int     (nbin, A->nseq);
+  max =(int*)vcalloc (nbin, sizeof (int));
+  used=(int*)vcalloc (nbin, sizeof (int));
+
+  for (maxnseq=0,s=1; s<A->nseq; s++)
+    {
+      int bin, n, t;
+
+      for (t=0, n=0,c=0; c<A->len_aln; c++)
+	{
+	  char c1=A->seq_al[0][c]; 
+	  char c2=A->seq_al[s][c]; 
+
+
+	  if (c1=='-' || c2=='-')continue;
+	  if (c1!=c2)n++;
+	  t++;
+	}
+      if (t==0)continue;
+      bin=((n*100)/t)%nbin;
+      lu[bin][max[bin]++]=s;
+      maxnseq++;
+    }
+
+  fp=vfopen (tmp, "w");
+  fprintf (fp, ">%s\n%s\n",A->name[0], A->seq_al[0]);
+
+  newn=0;
+  while ( newn<maxnseq && newn<ntrim)
+    {
+      for (bin=0; bin<nbin; bin++)
+	{
+	  if (used[bin]==max[bin])continue;
+	  else s=lu[bin][used[bin]++];
+	  fprintf (fp, ">%s\n%s\n",A->name[s], A->seq_al[s]);
+	  newn++;
+	}
+    }
+  vfclose (fp);
+
+  vfree (max);
+  vfree (used);
+  free_int (lu, -1);
+  return quick_read_fasta_aln (A, tmp);
+}
+
+
 
-Sequence * regtrim (Sequence *S, NT_node T, int N)
+Sequence  * regtrim (Sequence *S, NT_node T, int N)
 {
   NT_node *CL, *NL;
   int left, right, nc,nn, a,s,terminal;

lib/io_lib/tree_util.h

@@ -388,7 +388,7 @@ char *kmsa2msa (Sequence *S,KT_node *KL, int n);
 int ktree2klist (KT_node K, KT_node *KL, int *n);
 KT_node tree2ktree (NT_node ROOT,NT_node T,Sequence *S, int N);
 Sequence* regtrim( Sequence *S,NT_node T,int N);
-
+Alignment * sorttrim (Alignment *A,int ntrim);
 KT_node *free_ktree (KT_node k);
 char * kmsa2msa_d (Sequence *S,KT_node K, int max, int *cn);
 #endif

lib/util_lib/aln_convertion_util.c

@@ -6277,6 +6277,74 @@ char *trim_template_file (char *file, Sequence *S);//Remove from template file a
  * \param[in,out] S Sequence object, will be modified.
  * \param[in] template_list String containing the template file or commands how to get one
  */
+static int ntemp;
+Sequence * seq2mmseq_template_seq(Sequence *S,  Fname *F)
+{
+  /*Expected format for the template file:
+    >seq_name _X_ Target_template
+    X: S for Structures
+    G for genomes (Exoset)
+    When alternative templates are given for a sequence, the first one superseeds all the others
+  */
+
+
+  /*Fill the sequences*/
+  /*1: No template*/
+  char buf[1000];
+
+  int PmC,PmI,PMI;
+  int BmC,BmI,BMI, Trim;
+  char *server;
+  char *pdb_db,*prot_db;
+  char pdb_type[100];
+  char *p;
+  int remove_template_file=0;
+  static char *seqdb;
+
+  static char *seq=vtmpnam (NULL);
+  static char *outfile=vtmpnam(NULL);
+  static char *tf=NULL;
+  static char *command;
+  ntemp++;
+
+  remove_template_file=get_int_variable ("remove_template_file");
+  server=get_string_variable ("blast_server");
+  pdb_db=get_string_variable ("pdb_db");
+  prot_db=get_string_variable ("prot_db");         
+
+  PmI=get_int_variable ("pdb_min_sim");
+  PMI=get_int_variable ("pdb_max_sim");
+  PmC=get_int_variable ("pdb_min_cov");
+
+  BmI=get_int_variable ("prot_min_sim");
+  BMI=get_int_variable ("prot_max_sim");
+  BmC=get_int_variable ("prot_min_cov");
+  Trim=get_int_variable("psitrim");
+
+  output_fasta_seqS(seq,S);
+  if (!F)F=parse_fname (S->file[0]);
+
+
+
+  tf=csprintf (tf, "%s%s_F_%d.template_list", F->path,F->name,ntemp);
+  fprintf ( stderr, "\n! Running MMSEQ against %s -- This may take a while...\n", prot_db);
+  command=csprintf ( command, "t_coffee -other_pg mmseqs2prf.pl -q %s -db %s -o %s -template_file %s  -cachedb %s -quiet", seq, prot_db,outfile, tf, get_cache_dir());
+  printf_system (command);
+  if ( check_file_exists (tf) && format_is_fasta(tf))
+	{
+	  S=seq2template_seq (S,tf, F);
+	  trim_template_file (tf,S);
+	}
+  else
+    {
+
+      add_warning (stderr, "Could not Run %s to find templates[%s](unforked mode)\n",command, PROGRAM);
+      return NULL;
+    }
+
+  vfree (command);
+  return S;
+}
 Sequence * seq2template_seq ( Sequence *S, char *template_list, Fname *F)
 {
   /*Expected format for the template file:
@@ -6314,6 +6382,8 @@ Sequence * seq2template_seq ( Sequence *S, char *template_list, Fname *F)
   BmC=get_int_variable ("prot_min_cov");
   Trim=get_int_variable("psitrim");
 
+  if (template_list && strm(template_list, "MMSEQ"))return seq2mmseq_template_seq(S,F);
+
 
   if (strm (prot_db, "dataset") || strm (prot_db, "self"))
     {
@@ -6660,7 +6730,7 @@ Sequence * seq2template_seq ( Sequence *S, char *template_list, Fname *F)
 
   else if (strstr (template_list, "SCRIPT_"))
     {
-	  char x[299];
+      char x[299];
       char *tmp1,*command;
       Alignment *A;
       char outfile[1000];

lib/util_lib/aln_convertion_util.h

@@ -260,7 +260,7 @@ Sequence * display_seq_template_files (Sequence *S);
 Sequence * handle_seq_template_file (Sequence *S, char *mode);
 int handle_X_template_files ( X_template *T, char *mode);
 
-
+Sequence * seq2mmseq_template_seq(Sequence *S,  Fname *F);
 Sequence * seq2template_seq ( Sequence *S, char *template_file, Fname *F);
 char * seq2template_file (Sequence *S, char *file);
 int seq2template_file2 (Sequence *S, char *file, char *mode);

lib/util_lib/reformat.c

@@ -13128,6 +13128,11 @@ void modify_data  (Sequence_data_struc *D1in, Sequence_data_struc *D2in, Sequenc
 	   D1->S=aln2seq (D1->A);
 	 }
 
+       else if ( strm (action, "sorttrim"))
+	 {
+	   if (!D1->A)printf_exit (EXIT_FAILURE,stderr,"\nERROR: sorttrim requires an MSA as input [FATAL:%s]", PROGRAM);
+	   D1->A=sorttrim (D1->A, atoi(action_list[1]));
+	 }
        else if ( strm (action, "regtrim"))
 	 {
 	   int ns, p;

lib/version/build_version.version

@@ -1 +1 @@
-19
+20

lib/version/github.version

@@ -1 +1 @@
-* master 70f594b undocumented beta release tested with beta tests
+* master 8ffe5eb undocumented beta release tested with beta tests

lib/version/version_number.version

@@ -1 +1 @@
-Version_13.45.19.70f594b
+Version_13.45.20.8ffe5eb