/**
* @brief Sort sequences by length
*
* @param[out] prMSeq
* mseq to sort by length
* @param[out] cOrder
* Sorting order. 'd' for descending, 'a' for ascending.
*
*
*/
void
SortMSeqByLength(mseq_t *prMSeq, const char cOrder)
{
int *piSeqLen;
int *piOrder;
int iSeqIndex;
mseq_t *prMSeqCopy = NULL;
assert('a'==cOrder || 'd'==cOrder);
Log(&rLog, LOG_WARN,
"FIXME: This modifies sequence ordering. Might not be what user wants. Will change output order as well");
piSeqLen = (int *) CKMALLOC(prMSeq->nseqs * sizeof(int));
piOrder = (int *) CKMALLOC(prMSeq->nseqs * sizeof(int));
for (iSeqIndex=0; iSeqIndex<prMSeq->nseqs; iSeqIndex++) {
piSeqLen[iSeqIndex] = prMSeq->sqinfo[iSeqIndex].len;
}
QSortAndTrackIndex(piOrder, piSeqLen, prMSeq->nseqs, cOrder, FALSE);
CopyMSeq(&prMSeqCopy, prMSeq);
for (iSeqIndex=0; iSeqIndex<prMSeq->nseqs; iSeqIndex++) {
/* copy mseq entry
*/
CKFREE(prMSeq->seq[iSeqIndex]);
prMSeq->seq[iSeqIndex] = CkStrdup(prMSeqCopy->seq[piOrder[iSeqIndex]]);
CKFREE(prMSeq->orig_seq[iSeqIndex]);
prMSeq->orig_seq[iSeqIndex] = CkStrdup(prMSeqCopy->orig_seq[piOrder[iSeqIndex]]);
SeqinfoCopy(&prMSeq->sqinfo[iSeqIndex], &prMSeqCopy->sqinfo[piOrder[iSeqIndex]]);
}
CKFREE(piSeqLen);
CKFREE(piOrder);
FreeMSeq(&prMSeqCopy);
return;
}
/**
*
* @brief the 'real' main function
*
*/
int
MyMain(int argc, char **argv)
{
mseq_t *prMSeq = NULL;
mseq_t *prMSeqProfile1 = NULL;
mseq_t *prMSeqProfile2 = NULL;
cmdline_opts_t cmdline_opts;
/* Must happen first: setup logger */
LogDefaultSetup(&rLog);
/*Log(&rLog, LOG_WARN, "This is a non-public realase of %s. Please do not distribute.", PACKAGE_NAME);*/
/*Log(&rLog, LOG_WARN, "This is a beta version of %s, for protein only.", PACKAGE_NAME);*/ /* FS, r237 -> 238 */
SetDefaultUserOpts(&(cmdline_opts));
ParseCommandLine(&cmdline_opts, argc, argv);
if (NULL != cmdline_opts.pcLogFile) {
prLogFile = fopen(cmdline_opts.pcLogFile, "w");
LogSetFP(&rLog, LOG_INFO, prLogFile);
LogSetFP(&rLog, LOG_VERBOSE, prLogFile);
LogSetFP(&rLog, LOG_DEBUG, prLogFile);
}
InitClustalOmega(cmdline_opts.iThreads);
if (rLog.iLogLevelEnabled < LOG_INFO) {
PrintUserOpts(LogGetFP(&rLog, LOG_INFO), & cmdline_opts);
PrintAlnOpts(LogGetFP(&rLog, LOG_INFO), & (cmdline_opts.aln_opts));
}
/* Read sequence file
*
*/
if (NULL != cmdline_opts.pcSeqInfile) {
NewMSeq(&prMSeq);
if (ReadSequences(prMSeq, cmdline_opts.pcSeqInfile,
cmdline_opts.iSeqType, cmdline_opts.iSeqInFormat,
cmdline_opts.iMaxNumSeq, cmdline_opts.iMaxSeqLen)) {
Log(&rLog, LOG_FATAL, "Reading sequence file '%s' failed", cmdline_opts.pcSeqInfile);
}
#if TRACE
{
int iAux;
for (iAux=0; iAux<prMSeq->nseqs; iAux++) {
Log(&rLog, LOG_FORCED_DEBUG, "seq no %d: seq = %s", iAux, prMSeq->seq[iAux]);
LogSqInfo(&prMSeq->sqinfo[iAux]);
}
}
#endif
}
/* k-tuple pairwise distance calculation seg-faults if
* only one sequence, simply exit early.
* note that for profile/profile alignment prMSeq is NULL
* FS, r222->r223 */
if (prMSeq && (prMSeq->nseqs <= 1)){
Log(&rLog, LOG_FATAL, "File '%s' contains %d sequence%s, nothing to align",
cmdline_opts.pcSeqInfile, prMSeq->nseqs, 1==prMSeq->nseqs?"":"s");
}
/* Dealign if requested and neccessary
*/
if (NULL != prMSeq) {
if (TRUE == prMSeq->aligned && cmdline_opts.bDealignInputSeqs) {
Log(&rLog, LOG_INFO, "Dealigning already aligned input sequences as requested.");
DealignMSeq(prMSeq);
}
}
/* Read profile1
*
*/
if (NULL != cmdline_opts.pcProfile1Infile) {
NewMSeq(&prMSeqProfile1);
if (ReadSequences(prMSeqProfile1, cmdline_opts.pcProfile1Infile,
cmdline_opts.iSeqType, cmdline_opts.iSeqInFormat,
cmdline_opts.iMaxNumSeq, cmdline_opts.iMaxSeqLen)) {
Log(&rLog, LOG_FATAL, "Reading sequences from profile file '%s' failed",
cmdline_opts.pcProfile1Infile);
}
/* FIXME: commented out. FS, r240 -> r241
* for explanation see below */
/*if (1==prMSeqProfile1->nseqs) {
Log(&rLog, LOG_FATAL, "'%s' contains only one sequence and can therefore not be used as a profile",
cmdline_opts.pcProfile1Infile);
}*/
if (FALSE == prMSeqProfile1->aligned) {
Log(&rLog, LOG_FATAL, "Sequences in '%s' are not aligned, i.e. this is not a profile",
cmdline_opts.pcProfile1Infile);
}
}
/* Read profile2
*
*/
if (NULL != cmdline_opts.pcProfile2Infile) {
NewMSeq(&prMSeqProfile2);
if (ReadSequences(prMSeqProfile2, cmdline_opts.pcProfile2Infile,
cmdline_opts.iSeqType, cmdline_opts.iSeqInFormat,
cmdline_opts.iMaxNumSeq, cmdline_opts.iMaxSeqLen)) {
Log(&rLog, LOG_FATAL, "Reading sequences from profile file '%s' failed",
cmdline_opts.pcProfile2Infile);
}
/* FIXME: there is no (clean) way to align a single sequence to a profile.
* if we go down the -i route, it causes a seg-fault in the pair-wise
* k-tuple distance calculation. However, single sequences can be
* understood as 1-profiles. Therefore we have to allow for 1-profiles.
* FS, r240 -> r241
*/
/*if (1==prMSeqProfile2->nseqs) {
Log(&rLog, LOG_FATAL, "'%s' contains only one sequence and can therefore not be used as a profile",
cmdline_opts.pcProfile2Infile);
}*/
if (FALSE == prMSeqProfile1->aligned) {
Log(&rLog, LOG_FATAL, "Sequences in '%s' are not aligned, i.e. this is not a profile",
cmdline_opts.pcProfile2Infile);
}
}
/* Depending on the input we got perform
*
* (i) normal alignment: seq + optional profile
* or
* (ii) profile profile alignment
*
*/
if (NULL != prMSeq) {
if (Align(prMSeq, prMSeqProfile1, & cmdline_opts.aln_opts)) {
Log(&rLog, LOG_FATAL, "An error occured during the alignment");
}
if (WriteAlignment(prMSeq, cmdline_opts.pcAlnOutfile,
cmdline_opts.iAlnOutFormat)) {
Log(&rLog, LOG_FATAL, "Could not save alignment to %s", cmdline_opts.pcAlnOutfile);
}
#if 0
{
bool bSampling = FALSE; /* better set to TRUE for many sequences */
bool bReportAll = TRUE;
AliStat(prMSeq, bSampling, bReportAll);
}
#endif
} else if (NULL != prMSeqProfile1 && NULL != prMSeqProfile2) {
if (AlignProfiles(prMSeqProfile1, prMSeqProfile2,
cmdline_opts.aln_opts.rHhalignPara)) {
Log(&rLog, LOG_FATAL, "An error occured during the alignment");
}
if (WriteAlignment(prMSeqProfile1, cmdline_opts.pcAlnOutfile,
cmdline_opts.iAlnOutFormat)) {
Log(&rLog, LOG_FATAL, "Could not save alignment to %s", cmdline_opts.pcAlnOutfile);
}
}
/* cleanup
*/
if (NULL != prMSeq) {
FreeMSeq(&prMSeq);
}
if (NULL != prMSeqProfile1) {
FreeMSeq(&prMSeqProfile1);
}
if (NULL != prMSeqProfile2) {
FreeMSeq(&prMSeqProfile2);
}
FreeUserOpts(&cmdline_opts);
Log(&rLog, LOG_DEBUG, "Successful program exit");
if (NULL != cmdline_opts.pcLogFile) {
fclose(prLogFile);
}
return EXIT_SUCCESS;
}