int
main(int argc, char **argv)
{
ESL_GETOPTS *go = esl_getopts_CreateDefaultApp(options, 1, argc, argv, banner, usage);
char *msafile = esl_opt_GetArg(go, 1);
ESL_ALPHABET *abc = NULL;
int infmt = eslMSAFILE_UNKNOWN;
ESLX_MSAFILE *afp = NULL;
ESL_MSA *msa = NULL;
FILE *ofp = stdout;
int nali = 0;
int namewidth;
double pid;
int nid, n;
int i,j;
int status;
/* allow user to assert the input MSA alphabet */
if (esl_opt_GetBoolean(go, "--rna")) abc = esl_alphabet_Create(eslRNA);
else if (esl_opt_GetBoolean(go, "--dna")) abc = esl_alphabet_Create(eslDNA);
else if (esl_opt_GetBoolean(go, "--amino")) abc = esl_alphabet_Create(eslAMINO);
/* allow user to assert the input MSA format */
if (esl_opt_IsOn(go, "--informat") &&
(infmt = eslx_msafile_EncodeFormat(esl_opt_GetString(go, "--informat"))) == eslMSAFILE_UNKNOWN)
esl_fatal("%s is not a valid MSA file format for --informat", esl_opt_GetString(go, "--informat"));
/* digital open */
if ( ( status = eslx_msafile_Open(&abc, msafile, NULL, infmt, NULL, &afp)) != eslOK)
eslx_msafile_OpenFailure(afp, status);
while ((status = eslx_msafile_Read(afp, &msa)) == eslOK)
{
nali++;
namewidth = esl_str_GetMaxWidth(msa->sqname, msa->nseq);
for (i = 0; i < msa->nseq; i++)
for (j = i+1; j < msa->nseq; j++)
{
esl_dst_XPairId(abc, msa->ax[i], msa->ax[j], &pid, &nid, &n);
fprintf(ofp, "%-*s %-*s %6.2f %6d %6d\n", namewidth, msa->sqname[i], namewidth, msa->sqname[j], pid*100.0, nid, n);
}
esl_msa_Destroy(msa);
}
if (nali == 0 || status != eslEOF) eslx_msafile_ReadFailure(afp, status);
eslx_msafile_Close(afp);
esl_alphabet_Destroy(abc);
esl_getopts_Destroy(go);
return 0;
}
/* Function: esl_msafile_psiblast_Write()
* Synopsis: Write an MSA to a stream in PSI-BLAST format
*
* Purpose: Write alignment <msa> in NCBI PSI-BLAST format to
* stream <fp>.
*
* The <msa> should have a valid reference line <msa->rf>,
* with alphanumeric characters marking consensus (match)
* columns, and non-alphanumeric characters marking
* nonconsensus (insert) columns. If it does not have RF
* annotation, then the first sequence in the <msa>
* defines the "consensus".
*
* PSI-BLAST format allows only one symbol ('-') for gaps,
* and cannot represent missing data symbols (Easel's
* '~'). Any missing data symbols are converted to gaps.
*
* Args: fp - open output stream
* msa - MSA to write
*
* Returns: <eslOK> on success.
*
* Throws: <eslEMEM> on allocation failure.
* <eslEWRITE> on any system write failure, such as filled disk.
*/
int
esl_msafile_psiblast_Write(FILE *fp, const ESL_MSA *msa)
{
char *buf = NULL;
int cpl = 60;
int acpl;
int i;
int sym;
int64_t pos, bpos;
int maxnamewidth = esl_str_GetMaxWidth(msa->sqname, msa->nseq);
int is_consensus;
int is_residue;
int status;
ESL_ALLOC(buf, sizeof(char) * (cpl+1));
for (pos = 0; pos < msa->alen; pos += cpl)
{
for (i = 0; i < msa->nseq; i++)
{
acpl = (msa->alen - pos > cpl)? cpl : msa->alen - pos;
#ifdef eslAUGMENT_ALPHABET
if (msa->abc)
{
for (bpos = 0; bpos < acpl; bpos++)
{
sym = msa->abc->sym[msa->ax[i][pos + bpos + 1]];
is_residue = esl_abc_XIsResidue(msa->abc, msa->ax[i][pos+bpos+1]);
if (msa->rf) is_consensus = (isalnum(msa->rf[pos + bpos]) ? TRUE : FALSE);
else is_consensus = (esl_abc_XIsResidue(msa->abc, msa->ax[0][pos+bpos+1]) ? TRUE : FALSE);
if (is_consensus) { buf[bpos] = (is_residue ? toupper(sym) : '-'); }
else { buf[bpos] = (is_residue ? tolower(sym) : '-'); }
}
}
#endif
if (! msa->abc)
{
for (bpos = 0; bpos < acpl; bpos++)
{
sym = msa->aseq[i][pos + bpos];
is_residue = isalnum(sym);
if (msa->rf) is_consensus = (isalnum(msa->rf[pos + bpos]) ? TRUE : FALSE);
else is_consensus = (isalnum(msa->aseq[0][pos+bpos]) ? TRUE : FALSE);
if (is_consensus) { buf[bpos] = (is_residue ? toupper(sym) : '-'); }
else { buf[bpos] = (is_residue ? tolower(sym) : '-'); }
}
}
buf[acpl] = '\0';
if (fprintf(fp, "%-*s %s\n", maxnamewidth, msa->sqname[i], buf) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "psiblast msa write failed");
} /* end loop over sequences */
if (pos + cpl < msa->alen)
{ if (fputc('\n', fp) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "psiblast msa write failed"); }
}
free(buf);
return eslOK;
ERROR:
if (buf) free(buf);
return status;
}
