/* msa_shuffling()
* SRE, Tue Jan 22 08:39:51 2008 [Market Street Cafe, Leesburg]
*
* Shuffling multiple sequence alignments
*/
static int
msa_shuffling(ESL_GETOPTS *go, ESL_RANDOMNESS *r, FILE *ofp, int outfmt)
{
char *msafile = esl_opt_GetArg(go, 1);
int infmt = eslMSAFILE_UNKNOWN;
ESL_MSAFILE *afp = NULL;
ESL_MSA *msa = NULL;
ESL_MSA *shuf = NULL;
int N = esl_opt_GetInteger(go, "-N");
int i;
int status, mstatus;
status = esl_msafile_Open(msafile, infmt, NULL, &afp);
if (status == eslENOTFOUND) esl_fatal("Alignment file %s isn't readable\n", msafile);
else if (status == eslEFORMAT) esl_fatal("Couldn't determine format of %s\n", msafile);
else if (status != eslOK) esl_fatal("Alignment file open failed (error %d)\n", status);
while ((mstatus = esl_msa_Read(afp, &msa)) != eslEOF)
{
if (status == eslEFORMAT) esl_fatal("Alignment file parse error:\n%s\n", afp->errbuf);
else if (status == eslEINVAL) esl_fatal("Alignment file parse error:\n%s\n", afp->errbuf);
else if (status != eslOK) esl_fatal("Alignment file read failed with error code %d\n", status);
shuf = esl_msa_Clone(msa);
for (i = 0; i < N; i++)
{
if (esl_opt_GetBoolean(go, "--boot")) esl_msashuffle_Bootstrap(r, msa, shuf);
else esl_msashuffle_Shuffle (r, msa, shuf);
/* Set the name of the shuffled alignment */
if (msa->name != NULL) {
if (esl_opt_GetBoolean(go, "--boot")) {
if (N > 1) esl_msa_FormatName(shuf, "%s-sample-%d", msa->name, i);
else esl_msa_FormatName(shuf, "%s-sample", msa->name);
} else {
if (N > 1) esl_msa_FormatName(shuf, "%s-shuffle-%d", msa->name, i);
else esl_msa_FormatName(shuf, "%s-shuffle", msa->name);
}
} else {
if (esl_opt_GetBoolean(go, "--boot")) {
if (N > 1) esl_msa_FormatName(shuf, "sample-%d", i);
else esl_msa_FormatName(shuf, "sample");
} else {
if (N > 1) esl_msa_FormatName(shuf, "shuffle-%d", i);
else esl_msa_FormatName(shuf, "shuffle");
}
}
esl_msa_Write(ofp, shuf, outfmt);
}
esl_msa_Destroy(shuf);
esl_msa_Destroy(msa);
}
return eslOK;
}
/* msa_shuffling()
*
* Shuffling multiple sequence alignments
*/
static int
msa_shuffling(ESL_GETOPTS *go, ESL_RANDOMNESS *r, FILE *ofp, int outfmt)
{
char *msafile = esl_opt_GetArg(go, 1);
int infmt = eslMSAFILE_UNKNOWN;
ESL_MSAFILE *afp = NULL;
ESL_MSA *msa = NULL;
ESL_MSA *shuf = NULL;
int N = esl_opt_GetInteger(go, "-N");
int i;
int status;
if ( (status = esl_msafile_Open(NULL, msafile, NULL, infmt, NULL, &afp)) != eslOK)
esl_msafile_OpenFailure(afp, status);
while ((status = esl_msafile_Read(afp, &msa)) != eslEOF)
{
if (status != eslOK) esl_msafile_ReadFailure(afp, status);
shuf = esl_msa_Clone(msa);
for (i = 0; i < N; i++)
{
if (esl_opt_GetBoolean(go, "--boot")) esl_msashuffle_Bootstrap(r, msa, shuf);
else esl_msashuffle_Shuffle (r, msa, shuf);
/* Set the name of the shuffled alignment */
if (msa->name != NULL) {
if (esl_opt_GetBoolean(go, "--boot")) {
if (N > 1) esl_msa_FormatName(shuf, "%s-sample-%d", msa->name, i);
else esl_msa_FormatName(shuf, "%s-sample", msa->name);
} else {
if (N > 1) esl_msa_FormatName(shuf, "%s-shuffle-%d", msa->name, i);
else esl_msa_FormatName(shuf, "%s-shuffle", msa->name);
}
} else {
if (esl_opt_GetBoolean(go, "--boot")) {
if (N > 1) esl_msa_FormatName(shuf, "sample-%d", i);
else esl_msa_FormatName(shuf, "sample");
} else {
if (N > 1) esl_msa_FormatName(shuf, "shuffle-%d", i);
else esl_msa_FormatName(shuf, "shuffle");
}
}
esl_msafile_Write(ofp, shuf, afp->format);
}
esl_msa_Destroy(shuf);
esl_msa_Destroy(msa);
}
esl_msafile_Close(afp);
return eslOK;
}
