コード例 #1
0
ファイル: esl_msafile_a2m.c プロジェクト: EddyRivasLab/easel
/* Function:  esl_msafile_a2m_GuessAlphabet()
 * Synopsis:  Guess the alphabet of an open A2M MSA file.
 *
 * Purpose:   Guess the alpbabet of the sequences in open
 *            A2M format MSA file <afp>.
 *            
 *            On a normal return, <*ret_type> is set to <eslDNA>,
 *            <eslRNA>, or <eslAMINO>, and <afp> is reset to its
 *            original position.
 *
 * Args:      afp      - open A2M format MSA file
 *            ret_type - RETURN: <eslDNA>, <eslRNA>, or <eslAMINO>       
 *
 * Returns:   <eslOK> on success.
 *            <eslENOALPHABET> if alphabet type can't be determined.
 *            In either case, <afp> is rewound to the position it
 *            started at.
 *
 * Throws:    <eslEMEM> on allocation error.
 *            <eslESYS> on failures of fread() or other system calls
 */
int
esl_msafile_a2m_GuessAlphabet(ESL_MSAFILE *afp, int *ret_type)
{
  int       alphatype     = eslUNKNOWN;
  esl_pos_t anchor        = -1;
  int       threshold[3]  = { 500, 5000, 50000 }; /* we check after 500, 5000, 50000 residues; else we go to EOF */
  int       nsteps        = 3;
  int       step          = 0;
  int       nres          = 0;
  int       x;
  int64_t   ct[26];
  char     *p;
  esl_pos_t n, pos;
  int       status;

  for (x = 0; x < 26; x++) ct[x] = 0;

  anchor = esl_buffer_GetOffset(afp->bf);
  if ((status = esl_buffer_SetAnchor(afp->bf, anchor)) != eslOK) { status = eslEINCONCEIVABLE; goto ERROR; } /* [eslINVAL] can't happen here */

  while ( (status = esl_buffer_GetLine(afp->bf, &p, &n)) == eslOK)
    {
      while (n && isspace(*p)) { p++; n--; }
      if    (!n || *p == '>') continue;

      for (pos = 0; pos < n; pos++)
	if (isalpha(p[pos])) {
	  x = toupper(p[pos]) - 'A'; 
	  ct[x]++;
	  nres++;
	}

      /* try to stop early, checking after 500, 5000, and 50000 residues: */
      if (step < nsteps && nres > threshold[step]) {
	if ((status = esl_abc_GuessAlphabet(ct, &alphatype)) == eslOK) goto DONE; /* (eslENOALPHABET) */
	step++;
      }
    }
  if (status != eslEOF) goto ERROR; /* [eslEMEM,eslESYS,eslEINCONCEIVABLE] */
  status = esl_abc_GuessAlphabet(ct, &alphatype); /* (eslENOALPHABET) */

  /* deliberate flowthrough...*/
 DONE:
  esl_buffer_SetOffset(afp->bf, anchor);   /* Rewind to where we were. */
  esl_buffer_RaiseAnchor(afp->bf, anchor);
  *ret_type = alphatype;
  return status;

 ERROR:
  if (anchor != -1) {
    esl_buffer_SetOffset(afp->bf, anchor);
    esl_buffer_RaiseAnchor(afp->bf, anchor);
  }
  *ret_type = eslUNKNOWN;
  return status;
}
コード例 #2
0
ファイル: esl_msafile_psiblast.c プロジェクト: appris/appris
/* Function:  esl_msafile_psiblast_GuessAlphabet()
 * Synopsis:  Guess the alphabet of an open PSI-BLAST MSA file.
 *
 * Purpose:   Guess the alpbabet of the sequences in open
 *            PSI-BLAST format MSA file <afp>.
 *            
 *            On a normal return, <*ret_type> is set to <eslDNA>,
 *            <eslRNA>, or <eslAMINO>, and <afp> is reset to its
 *            original position.
 *
 * Args:      afp      - open PSI-BLAST format MSA file
 *            ret_type - RETURN: <eslDNA>, <eslRNA>, or <eslAMINO>       
 *
 * Returns:   <eslOK> on success.
 *            <eslENOALPHABET> if alphabet type can't be determined.
 *            In either case, <afp> is rewound to the position it
 *            started at.
 */
int
esl_msafile_psiblast_GuessAlphabet(ESLX_MSAFILE *afp, int *ret_type)
{
  int       alphatype     = eslUNKNOWN;
  esl_pos_t anchor        = -1;
  int       threshold[3]  = { 500, 5000, 50000 }; /* we check after 500, 5000, 50000 residues; else we go to EOF */
  int       nsteps        = 3;
  int       step          = 0;
  int       nres          = 0;
  int       x;
  int64_t   ct[26];
  char     *p, *tok;
  esl_pos_t n,  toklen, pos;
  int       status;

  for (x = 0; x < 26; x++) ct[x] = 0;

  anchor = esl_buffer_GetOffset(afp->bf);
  if ((status = esl_buffer_SetAnchor(afp->bf, anchor)) != eslOK) { status = eslEINCONCEIVABLE; goto ERROR; } /* [eslINVAL] can't happen here */

  while ( (status = esl_buffer_GetLine(afp->bf, &p, &n)) == eslOK)
    {
      if ((status = esl_memtok(&p, &n, " \t", &tok, &toklen)) != eslOK) continue; /* blank lines */
      /* p now points to the rest of the sequence line, after a name */
      
      /* count characters into ct[] array */
      for (pos = 0; pos < n; pos++)
	if (isalpha(p[pos])) {
	  x = toupper(p[pos]) - 'A';
	  ct[x]++;
	  nres++; 
	}

      /* try to stop early, checking after 500, 5000, and 50000 residues: */
      if (step < nsteps && nres > threshold[step]) {
	if ((status = esl_abc_GuessAlphabet(ct, &alphatype)) == eslOK) goto DONE; /* (eslENOALPHABET) */
	step++;
      }
    }
  if (status != eslEOF) goto ERROR; /* [eslEMEM,eslESYS,eslEINCONCEIVABLE] */
  status = esl_abc_GuessAlphabet(ct, &alphatype); /* (eslENOALPHABET) */

 DONE:
  esl_buffer_SetOffset(afp->bf, anchor);   /* Rewind to where we were. */
  esl_buffer_RaiseAnchor(afp->bf, anchor);
  *ret_type = alphatype;
  return status;

 ERROR:
  if (anchor != -1) {
    esl_buffer_SetOffset(afp->bf, anchor);
    esl_buffer_RaiseAnchor(afp->bf, anchor);
  }
  *ret_type = eslUNKNOWN;
  return status;
}