undocumented beta release tested with beta tests

build/web-readme.txt

@@ -1,6 +1,6 @@
 T-Coffee distribution 
 =====================
-Version_13.45.24.7b3f015 #_#UPDATE_VERSION -- Populated by edit_version.pl
+Version_13.45.25.e3f346d #_#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:

compile/makefile

@@ -179,6 +179,7 @@ quote="'"'"
 SCRIPT_LIB_OBJECTS=\
 	msa2bootstrap.pl\
 	tc_generic_method.pl\
+	mmseqs2prf.pl\
 	dynamic.pl\
 	rnapdb2protpdb.pl\
 	generic_method.tc_method\
@@ -220,6 +221,10 @@ dynamic.pl:\
 	$(SCRIPT_LIB)/dynamic.pl
 	cp $(SCRIPT_LIB)/dynamic.pl .
 	echo "my $(dollar)program=$(quote)$(PROGRAM) ($(VERSION))$(quote);">> dynamic.pl
+mmseqs2prf.pl:\
+	$(SCRIPT_LIB)/mmseqs2prf.pl
+	cp $(SCRIPT_LIB)/mmseqs2prf.pl .
+	echo "my $(dollar)program=$(quote)$(PROGRAM) ($(VERSION))$(quote);">> mmseqs2prf.pl
 rnapdb2protpdb.pl:\
 	$(SCRIPT_LIB)/rnapdb2protpdb.pl
 	cp $(SCRIPT_LIB)/rnapdb2protpdb.pl .

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: c122ad66236c9fbda053fb251bddea29
+config: 552f711835f7ca8c141707ce05bcff5c
 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_13.45.24.7b3f015',
+    VERSION: 'Version_13.45.25.e3f346d',
     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_13.45.24.7b3f015 documentation</title>
+  <title>T-Coffee Version_13.45.25.e3f346d documentation</title>
 
 
 
@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                Version_13.45.24.7b3f015
+                Version_13.45.25.e3f346d
               </div>
 
 
@@ -716,7 +716,7 @@
 
       <li><a href="index.html#document-index">Docs</a> &raquo;</li>
 
-      <li>T-Coffee Version_13.45.24.7b3f015 documentation</li>
+      <li>T-Coffee Version_13.45.25.e3f346d documentation</li>
 
 
       <li class="wy-breadcrumbs-aside">

docs/conf.py

@@ -54,9 +54,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'Version_13.45.24.7b3f015' #_#UPDATE_VERSION_TAG1 -- Populated by edit_version.pl
+version = u'Version_13.45.25.e3f346d' #_#UPDATE_VERSION_TAG1 -- Populated by edit_version.pl
 # The full version, including alpha/beta/rc tags.
-release = u'Version_13.45.24.7b3f015' #_#UPDATE_VERSION_TAG2 -- Populated by edit_version.pl
+release = u'Version_13.45.25.e3f346d' #_#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

@@ -104,12 +104,13 @@ double scan_maxd (p3D *D)
 
 	      if (verbose())fprintf ( stderr, "\n!# scan        : +maxd %3d %-12s ==> RF vs reftree %5.2f Nsites: %5d", a, (strict)?"+strict_maxd":"+soft_maxd", (float) 100-rf,D->nsites);
 
-	      if ( rf>brf || (rf==brf && D->nsites>bnsites) || (rf==brf && (double)a>=bmaxd))
+	      if ((!getenv ("first_maxd_4_TCOFFEE") && (rf>brf || (rf==brf && D->nsites>bnsites) || (rf==brf && (double)a>=bmaxd))) || ((rf>brf)))
 		{
 		  brf=rf;
 		  bmaxd=(double)a;
 		  bstrict=strict;
 		  bnsites=D->nsites;
+		  fprintf (stderr, "***");
 		}
 	    }
 	  else

lib/util_lib/aln_convertion_util.c

@@ -6278,7 +6278,7 @@ char *trim_template_file (char *file, Sequence *S);//Remove from template file a
  * \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)
+Sequence * seq2mmseqs_template_seq(Sequence *S,  Fname *F)
 {
   /*Expected format for the template file:
     >seq_name _X_ Target_template
@@ -6305,6 +6305,7 @@ Sequence * seq2mmseq_template_seq(Sequence *S,  Fname *F)
   static char *outfile=vtmpnam(NULL);
   static char *tf=NULL;
   static char *command;
+  char *cache=get_cache_dir();
   ntemp++;
 
   remove_template_file=get_int_variable ("remove_template_file");
@@ -6326,9 +6327,9 @@ Sequence * seq2mmseq_template_seq(Sequence *S,  Fname *F)
 
 
 
-  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());
+  tf=csprintf (tf, "%s%s_R_%d.template_list", F->path,F->name,ntemp);
+  fprintf ( stderr, "\n! Running MMSEQS 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 -prot_min_sin %d -prot_max_sim %d -prot_min_cov %d -psitrim %d -quiet", seq, prot_db,cache, tf,cache, BmI, BMI, BmC, Trim);
   printf_system (command);
   if ( check_file_exists (tf) && format_is_fasta(tf))
 	{
@@ -6382,7 +6383,7 @@ 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 (template_list && strm(template_list, "MMSEQS"))return seq2mmseqs_template_seq(S,F);
 
 
   if (strm (prot_db, "dataset") || strm (prot_db, "self"))

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 * seq2mmseqs_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

@@ -225,7 +225,10 @@ int seq_reformat ( int argc, char **in_argv)
 		fprintf ( stdout, "\n     .......................! seq offset_value (0 by default)");
 		fprintf ( stdout, "\n     .....................Can extract as many positions as needed");
 		fprintf ( stdout, "\n     .....................seq=cons: measure positions on the full aln");
-		fprintf ( stdout, "\n     +cat_aln.............Concatenates the alignments input via -in and -in2");
+
+
+		fprintf ( stdout, "\n     +split.<N>............Split fasta file into smaller files\n");
+		fprintf ( stdout, "\n     +cat_aln..............Concatenates the alignments input via -in and -in2");
 		fprintf ( stdout, "\n     +cat_aln.............-if no -in2, -in is expected to be a list of alignments to concatenate");
 		fprintf ( stdout, "\n     +orthologous_cat..<mode>: mode=voronoi or nothing");
 		fprintf ( stdout, "\n     ......................-in: sequences from different species");
@@ -1610,7 +1613,7 @@ long *fasta2map(char *file)
   FILE *fp;
   int i=0;
   long pos=0;
-  char c,lc;
+  char c,lc,pc;
   long *map;
   int ml=1000;
   int a;
@@ -1634,16 +1637,18 @@ long *fasta2map(char *file)
 
   fp=vfopen(file, "r");
   pos=0;
+  pc='\n';
   while (fgets(buf,VERY_LONG_STRING,fp))
     {
       int d=0;
       while ((c=buf[d++])!='\0')
 	{
-	  if (c=='>')
+	  if (c=='>' && pc=='\n')
 	    {
 	      if (i>=ml){ml+=VERY_LONG_STRING; map=(long*)vrealloc (map, ml*sizeof (long));}
 	      map[i++]=pos;
 	    }
+	  pc=c;
 	  pos++;
 	}
     }
@@ -1681,6 +1686,45 @@ Alignment *reload_aln(Alignment *A)
   dump_msa (A,tmp);
   return quick_read_fasta_aln(A,tmp);
 }
+char *      split_fasta (char *file, int size)
+{
+  long *map;
+  int i, j,nseq, n;
+  FILE *fp=NULL;
+  char *split=NULL;
+
+  fprintf (stderr, "! Indexing started");
+  file2record_it(NULL,0, NULL);
+  map=fasta2map(file);
+  nseq=read_array_size_new (map)-1;
+  fprintf (stderr, "! Indexing Finished -- %d Sequences", nseq);
+  for(n=0,j=0,i=0;i<nseq; i++,j++)
+    {
+      char *s;
+
+      if (j==0|| j==size)
+	{
+	  j=0;
+	  fprintf (stdout, "%s.%d.split\n",file, n);
+	  split=csprintf(split,"%s.%d.split", file, n);
+	  if (fp){vfclose(fp);}
+	  fp=vfopen(split, "w");
+	  n++;
+	}
+      if ((s=file2record_it(file,i, map)))
+	{
+	  fprintf (fp, "%s",s);
+	}
+      else
+	{
+	  HERE ("FAILED to parse file. Possible file corruption [FATAL]");exit (0);
+	}
+    }
+  vfclose (fp);
+  vfree(map);
+  exit (EXIT_SUCCESS);
+  return NULL;
+}
 Alignment * quick_read_fasta_aln (Alignment *A, char *file)
 {
   long *map;
@@ -11071,7 +11115,8 @@ void modify_data  (Sequence_data_struc *D1in, Sequence_data_struc *D2in, Sequenc
 	   D2=D2in;
 	   DST=DSTin;
 	 }
-       if (!D1->A)D1->A=copy_aln (D1in->A, NULL);
+
+       if (D1 && !D1->A && D1in && D1in->A)D1->A=copy_aln (D1in->A, NULL);
 
        if (  strm(action, "seqnos"))
 	 {
@@ -11730,6 +11775,7 @@ void modify_data  (Sequence_data_struc *D1in, Sequence_data_struc *D2in, Sequenc
        else if ( strm(action, "min_maxd"))cputenv ("min_maxd_4_TCOFFEE=%s",ACTION(1));
        else if ( strm(action, "strict_maxd"))cputenv ("strict_maxd_4_TCOFFEE=%s",ACTION(1));
        else if ( strm(action, "soft_maxd"))cputenv ("soft_maxd_4_TCOFFEE=%s",ACTION(1));
+       else if ( strm(action, "first_maxd"))cputenv ("first_maxd_4_TCOFFEE=%s",ACTION(1));
 
        else if ( strm(action, "align_method"))
 	 {
@@ -12388,7 +12434,28 @@ void modify_data  (Sequence_data_struc *D1in, Sequence_data_struc *D2in, Sequenc
 	 {
 	   D1->A=orthologous_concatenate_aln (D1->A,D2->S, ACTION (1));
 	 }
+       else if ( strm (action, "split"))
+	 {
+	   char *file=split_fasta (ACTION(1), atoi (ACTION(2)));
+	   vfclose (display_file_content (NULL,file));
+	 }
+
+       else if (ACTION(1) && is_aln(ACTION(1)))
+	     {
+	         Alignment *B;
+		 int n=1;
 
+		 while (ACTION(n))
+		   {
+
+		     B=main_read_aln (ACTION(n), NULL);
+		     D1->A=concatenate_aln (D1->A, B, NULL);
+		     n++;
+		   }
+		 D1->S=aln2seq(D1->A);
+	     }
+
+
        else if ( strm (action, "cat_aln"))
 	 {
 	   /*D1->A=aln_cat ( D1->A, D2 ->A);*/

lib/util_lib/reformat.h

@@ -51,6 +51,7 @@ int fasta2nseq (char *file);
 
 Sequence  * quick_read_seq ( char *file);
 Alignment *reload_aln (Alignment*A);
+char *      split_fasta (char *file, int size);
 Alignment * quick_read_aln( char *name);//reads onl�y fasta and clustalw
 Alignment * quick_read_fasta_aln( Alignment *A,char *name);//reads onl�y fasta and clustalw
 Alignment * quick_read_aln_static( char *name);//reads onl�y fasta and clustalw

lib/version/build_version.version

@@ -1 +1 @@
-24
+25

lib/version/github.version

@@ -1 +1 @@
-* master 7b3f015 undocumented beta release tested with beta tests
+* master e3f346d undocumented beta release tested with beta tests

lib/version/version_number.version

@@ -1 +1 @@
-Version_13.45.24.7b3f015
+Version_13.45.25.e3f346d