Esempio n. 1
0
AlnBlock * Align_Sequences_ProteinBlockAligner(Sequence * one,Sequence * two,CompMat * comp,int bentry,int bexit,int b1exit,int b_self,int b_on,DPRunImpl * dpri)
{
  ComplexSequence * cone=NULL;
  ComplexSequence * ctwo=NULL;
  AlnBlock * alb= NULL;
  PackAln * pal=NULL;
  ComplexSequenceEvalSet * evalfunc = NULL;

  if( one == NULL || two == NULL || comp == NULL ) {
    warn("Passed in NULL objects into Align_Sequences_ProteinSmithWaterman!");
    return NULL;
  }

  if( one->type != SEQUENCE_PROTEIN ) {
    warn("Sequence %s is not typed as protein... ignoring!\n",one->name);
  }

  if( two->type != SEQUENCE_PROTEIN ) {
    warn("Sequence %s is not typed as protein... ignoring!\n",two->name);
  }


  evalfunc = default_aminoacid_ComplexSequenceEvalSet();
  
  cone = new_ComplexSequence(one,evalfunc);
  if( cone == NULL )
    goto cleanup;
  ctwo = new_ComplexSequence(two,evalfunc);
  if( ctwo == NULL )
    goto cleanup;

  pal = PackAln_bestmemory_ProteinBlockAligner(cone,ctwo,comp,bentry,b1exit,b_on,b_self,bexit,NULL,dpri);

  if( pal == NULL ) 
    goto cleanup;

  alb = convert_PackAln_to_AlnBlock_ProteinSW(pal);
  
  goto cleanup;

  cleanup :

  if( cone != NULL )
      free_ComplexSequence(cone);

  if( ctwo != NULL )
    free_ComplexSequence(ctwo);

  if( pal != NULL )
    free_PackAln(pal);

  if( evalfunc != NULL )
    free_ComplexSequenceEvalSet(evalfunc);

  return alb;

}
Esempio n. 2
0
AlnBlock * Align_Sequences_ProteinSmithWaterman(Sequence * one,Sequence * two,CompMat * comp,int gap,int ext,DPRunImpl * dpri)
{
  AlnBlock * out = NULL;
  ComplexSequenceEvalSet * evalfunc = NULL;
  ComplexSequence * query_cs = NULL;
  ComplexSequence * target_cs = NULL;
  PackAln * pal = NULL;

  if( one == NULL || two == NULL || comp == NULL ) {
    warn("Passed in NULL objects into Align_Sequences_ProteinSmithWaterman!");
    return NULL;
  }

  if( one->type != SEQUENCE_PROTEIN ) {
    warn("Sequence %s is not typed as protein... ignoring!\n",one->name);
  }

  if( two->type != SEQUENCE_PROTEIN ) {
    warn("Sequence %s is not typed as protein... ignoring!\n",two->name);
  }


  if( gap > 0 || ext > 0 ) {
    warn("Gap penalties %d,%d only make sense if they are negative",gap,ext);
    return NULL;
  }

  evalfunc = default_aminoacid_ComplexSequenceEvalSet();
  
  query_cs = new_ComplexSequence(one,evalfunc);
  if( query_cs == NULL )
    goto cleanup;
  target_cs = new_ComplexSequence(two,evalfunc);
  if( target_cs == NULL )
    goto cleanup;

  pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp,gap,ext,NULL,dpri);
  if( pal == NULL ) 
    goto cleanup;

  out = convert_PackAln_to_AlnBlock_ProteinSW(pal);
  
  goto cleanup;

  cleanup :

    if( query_cs != NULL )
      free_ComplexSequence(query_cs);

  if( target_cs != NULL )
    free_ComplexSequence(target_cs);

  if( pal != NULL )
    free_PackAln(pal);

  if( evalfunc != NULL )
    free_ComplexSequenceEvalSet(evalfunc);

  return out;

}
Esempio n. 3
0
int main(int argc,char ** argv)
{
  int i;
  SequenceSet * in;
  Sequence * trans;
  ThreeStateDB * tsd;

  DPRunImpl * dpri;
  CodonTable * ct;

  int return_status;
  ThreeStateModel * tsm;
  ThreeStateScore * tss;
  Protein * hmmp;
  ComplexSequence * cs;
  ComplexSequenceEvalSet * cses;

  PackAln * pal;
  AlnBlock * alb;

  int show_align = 0;
  int show_alb   = 0;
  int show_verbose = 1;
  int show_trans = 0;

  ct = read_CodonTable_file("codon.table");

  cses = default_aminoacid_ComplexSequenceEvalSet();
  
  dpri = new_DPRunImpl_from_argv(&argc,argv);

  strip_out_boolean_def_argument(&argc,argv,"pretty",&show_align);

  strip_out_boolean_def_argument(&argc,argv,"alb",&show_alb);

  strip_out_boolean_def_argument(&argc,argv,"trans",&show_trans);

  if( argc != 3 ) {
    show_help(stdout);
    exit(63);
  }


  in = read_fasta_SequenceSet_file(argv[1]);

  tsd = HMMer2_ThreeStateDB(argv[2]);

  assert(in);
  assert(tsd);
  assert(in->len == 2);

  trans = translate_Sequence(in->set[0],ct);

  if( show_trans ) {
    write_fasta_Sequence(trans,stdout);
  }

  cs = new_ComplexSequence(trans,cses);

  open_ThreeStateDB(tsd);

  while( (tsm = read_TSM_ThreeStateDB(tsd,&return_status)) != NULL ) {
    fold_RandomModel_into_ThreeStateModel(tsm,tsm->rm);
    set_startend_policy_ThreeStateModel(tsm,TSM_local,10,1.0);

    tss = ThreeStateScore_from_ThreeStateModel(tsm);
    hmmp = pseudo_Protein_from_ThreeStateModel(tsm);

    pal = PackAln_bestmemory_ThreeStateLoop(tss,cs,NULL,dpri);
    alb = convert_PackAln_to_AlnBlock_ThreeStateLoop(pal);

    if( show_alb ) {
      show_flat_AlnBlock(alb,stdout);
    }

    if( show_align ) {
      write_pretty_seq_align(alb,hmmp->baseseq,trans,15,50,stdout);      
    }
    if( show_verbose ) {
      show_verbose_evo(alb,tsm,in->set[0],in->set[1],ct,stdout);
    }
      
  }
  

}
Esempio n. 4
0
int main(int argc,char ** argv)
{
  Sequence * query;
  Sequence * target;
  CompMat * comp;
  char * comp_file;
  int gap = (12);
  int ext = (2);
  int a = 120;
  int b = 10;
  int c = 3;
  ComplexSequence * query_cs;
  ComplexSequence * target_cs;
  ComplexSequenceEvalSet * evalfunc;

  boolean show_label_output = FALSE;
  boolean show_fancy_output = FALSE;
  boolean use_abc = FALSE;

  PackAln * pal;
  AlnBlock * alb;

  DPRunImpl * dpri = NULL;

  /*
   * Process command line options
   * -h or -help gives us help
   * -g for gap value (an int) - rely on commandline error processing
   * -e for ext value (an int) - rely on commandline error processing
   * -m for matrix (a char)
   * -l - label output
   * -f - fancy output
   *
   *
   * Use calls to commandline.h functions
   *
   */
  
  if( strip_out_boolean_argument(&argc,argv,"h") == TRUE || strip_out_boolean_argument(&argc,argv,"-help") == TRUE) {
    show_help(stdout);
    exit(1);
  }

  dpri = new_DPRunImpl_from_argv(&argc,argv);
  if( dpri == NULL ) {
    fatal("Unable to build DPRun implementation. Bad arguments");
  }

  show_label_output = strip_out_boolean_argument(&argc,argv,"l");
  show_fancy_output = strip_out_boolean_argument(&argc,argv,"f");


  /** if all FALSE, set fancy to TRUE **/

  if( show_label_output == FALSE ) 
    show_fancy_output = TRUE;


  (void) strip_out_integer_argument(&argc,argv,"g",&gap);
  (void) strip_out_integer_argument(&argc,argv,"e",&ext);
  (void) strip_out_integer_argument(&argc,argv,"a",&a);
  (void) strip_out_integer_argument(&argc,argv,"b",&b);
  (void) strip_out_integer_argument(&argc,argv,"c",&c);

  use_abc = strip_out_boolean_argument(&argc,argv,"abc"); 
  
  comp_file = strip_out_assigned_argument(&argc,argv,"m");
  if( comp_file == NULL)
    comp_file = "blosum62.bla";

  
  
  if( argc != 3 ) {
    warn("Must have two arguments for sequence 1 and sequence 2 %d",argc);
    show_help(stdout);
    exit(1);
  }
  
  /*
   * Read in two sequences
   */
  
  if( (query=read_fasta_file_Sequence(argv[1])) == NULL ) {
    fatal("Unable to read the sequence in file %s",argv[1]);
  }
  
  if( (target=read_fasta_file_Sequence(argv[2])) == NULL ) {
    fatal("Unable to read the sequence in file %s",argv[2]);
  }
  
  
  /*
   * Open a blosum matrix. This will be opened from WISECONFIGDIR
   * or WISEPERSONALDIR if it is not present in the current directory.
   */
  
  comp = read_Blast_file_CompMat(comp_file);
  
  if( comp == NULL ) {
    fatal("unable to read file %s",comp_file);
  }
  
  /* if abc - factor up matrix! */

  if( use_abc == TRUE ) {
    factor_CompMat(comp,10);
  }


  /*
   * Make an alignment. I don't care about the implementation:
   * hand it over to sw_wrap function to do it
   *
   */		 

  if( use_abc ) {
    evalfunc = default_aminoacid_ComplexSequenceEvalSet();
  
    query_cs = new_ComplexSequence(query,evalfunc);
    if( query_cs == NULL )
      fatal("Cannot build cs objects!");
    target_cs = new_ComplexSequence(target,evalfunc);
    if( target_cs == NULL )
      fatal("Cannot build cs objects!");

    pal = PackAln_bestmemory_abc(query_cs,target_cs,comp,-a,-b,-c,NULL,dpri);
    alb = convert_PackAln_to_AlnBlock_abc(pal);
    free_ComplexSequence(query_cs);
    free_ComplexSequence(target_cs);
  } else {
    alb = Align_Sequences_ProteinSmithWaterman(query,target,comp,-gap,-ext,dpri);
  }


  /*
   * show output. If multiple outputs, divide using //
   */


  if( show_label_output == TRUE ) {
    show_flat_AlnBlock(alb,stdout);
    puts("//\n");
  }

  if( show_fancy_output == TRUE ) {
    write_pretty_seq_align(alb,query,target,15,50,stdout);
    puts("//\n");
  }

  /*
   * Destroy the memory.
   */	

  free_Sequence(query);
  free_Sequence(target);
  free_CompMat(comp);
  free_AlnBlock(alb);

  return 0;
}
Esempio n. 5
0
int main(int argc,char ** argv)
{
  Sequence * query;
  Sequence * target;
  ComplexSequence * query_cs;
  ComplexSequence * target_cs;
  ComplexSequenceEvalSet  * evalfunc;
  CompMat * comp;
  char * comp_file;
  int gap = (12);
  int ext = (2);

  boolean show_raw_output = FALSE;
  boolean show_label_output = FALSE;
  boolean show_fancy_output = FALSE;
  boolean has_outputted = FALSE;

  PackAln * pal;
  AlnBlock * alb;
  
  /*
   * Process command line options
   * -h or -help gives us help
   * -g for gap value (an int) - rely on commandline error processing
   * -e for ext value (an int) - rely on commandline error processing
   * -m for matrix (a char)
   * -r - raw matrix output
   * -l - label output
   * -f - fancy output
   *
   *
   * Use calls to commandline.h functions
   *
   */
  
  if( strip_out_boolean_argument(&argc,argv,"h") == TRUE || strip_out_boolean_argument(&argc,argv,"-help") == TRUE) {
    show_help(stdout);
    exit(1);
  }

  show_raw_output = strip_out_boolean_argument(&argc,argv,"r");
  show_label_output = strip_out_boolean_argument(&argc,argv,"l");
  show_fancy_output = strip_out_boolean_argument(&argc,argv,"f");


  /** if all FALSE, set fancy to TRUE **/

  if( show_raw_output == FALSE && show_label_output == FALSE ) 
    show_fancy_output = TRUE;


  (void) strip_out_integer_argument(&argc,argv,"g",&gap);
  (void) strip_out_integer_argument(&argc,argv,"e",&ext);

  comp_file = strip_out_assigned_argument(&argc,argv,"m");
  if( comp_file == NULL)
    comp_file = "blosum62.bla";

  
  
  if( argc != 3 ) {
    warn("Must have two arguments for sequence 1 and sequence 2 %d",argc);
    show_help(stdout);
    exit(1);
  }
  
  /*
   * Read in two sequences
   */
  
  if( (query=read_fasta_file_Sequence(argv[1])) == NULL ) {
    fatal("Unable to read the sequence in file %s",argv[1]);
  }
  
  if( (target=read_fasta_file_Sequence(argv[2])) == NULL ) {
    fatal("Unable to read the sequence in file %s",argv[2]);
  }
  
  
  /*
   * Open a blosum matrix. This will be opened from WISECONFIGDIR
   * or WISEPERSONALDIR if it is not present in the current directory.
   */
  
  comp = read_Blast_file_CompMat(comp_file);
  
  if( comp == NULL ) {
    fatal("unable to read file %s",comp_file);
  }
  
  /*
   * Convert sequences to ComplexSequences: 
   * To do this we need an protein ComplexSequenceEvalSet
   *
   */
  
  evalfunc = default_aminoacid_ComplexSequenceEvalSet();
  
  query_cs = new_ComplexSequence(query,evalfunc);
  if( query_cs == NULL ) {
    fatal("Unable to make a protein complex sequence from %s",query->name);
  }
  
  target_cs = new_ComplexSequence(target,evalfunc);
  if( target_cs == NULL ) {
    fatal("Unable to make a protein complex sequence from %s",target->name);
  }
  
  /*
   * Make an alignment. I don't care about the implementation:
   * If the sequences are small enough then it should use explicit memory.
   * Long sequences should use divide and conquor methods.
   *
   * Calling PackAln_bestmemory_ProteinSW is the answer
   * This function decides on the best method considering the
   * memory and changes accordingly. It frees the matrix memory 
   * at the end as well.
   *
   */		 

  pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp,-gap,-ext,NULL);

  if( pal == NULL ) {
    fatal("Unable to make an alignment from %s and %s",query->name,target->name);
  }

  /*
   * ok, make other alignment forms, and be ready to show
   */



  alb = convert_PackAln_to_AlnBlock_ProteinSW(pal);


  /*
   * show output. If multiple outputs, divide using //
   */

  if( show_raw_output == TRUE ) {
    show_simple_PackAln(pal,stdout);
    puts("//\n");
  }

  if( show_label_output == TRUE ) {
    show_flat_AlnBlock(alb,stdout);
  }

  if( show_fancy_output == TRUE ) {
    write_pretty_seq_align(alb,query,target,15,50,stdout);
    puts("//\n");
  }

  /*
   * Destroy the memory.
   */	

  free_Sequence(query);
  free_Sequence(target);
  free_CompMat(comp);
  free_ComplexSequence(query_cs);
  free_ComplexSequence(target_cs);
  free_PackAln(pal);
  free_AlnBlock(alb);

  return 0;
}