Sequence * magic_trunc_Sequence(Sequence * seq,int start,int end)
{
Sequence * temp;
Sequence * out;
if( is_dna_Sequence(seq) == FALSE) {
warn("Cannot magic truncate on a non DNA sequence... type is %s",Sequence_type_to_string(seq->type));
return NULL;
}
if( start < 0 || end < 0 ) {
warn("Attempting a magic truncation on indices which are less than zero [%d:%d]. Clearly impossible",start,end);
return NULL;
}
if( start < end ) {
return trunc_Sequence(seq,start,end);
}
else {
temp = trunc_Sequence(seq,end,start);
if( temp == NULL ) {
warn("Unable to truncate sequence");
return NULL;
}
out = reverse_complement_Sequence(temp);
free_Sequence(temp);
return out;
}
}
cDNADB * new_cDNADB_from_single_seq(cDNA * seq)
{
ComplexSequence * cs,*cs_rev;
Sequence * temp;
ComplexSequenceEvalSet * cses;
cses = default_cDNA_ComplexSequenceEvalSet();
cs = new_ComplexSequence(seq->baseseq,cses);
temp = reverse_complement_Sequence(seq->baseseq);
cs_rev = new_ComplexSequence(temp,cses);
free_Sequence(temp);
free_ComplexSequenceEvalSet(cses);
return new_cDNADB_from_forrev_cseq(cs,cs_rev);
}
int main(int argc,char ** argv)
{
Sequence * in;
Sequence * rev;
while( in = read_fasta_Sequence(stdin) ) {
in->type = SEQUENCE_DNA;
rev = reverse_complement_Sequence(in);
write_fasta_Sequence(rev,stdout);
free_Sequence(in);
free_Sequence(rev);
}
}
cDNA * get_cDNA_from_cDNADB(cDNADB * cdnadb,DataEntry * de)
{
Sequence * seq;
Sequence * temp;
if( cdnadb == NULL ) {
warn("Cannot get entry from a null database");
return NULL;
}
if( de == NULL ) {
warn("Cannot get entry with a null dataentry");
return NULL;
}
if( cdnadb->is_single_seq == TRUE ) {
if( de->is_reversed == TRUE )
return cDNA_from_Sequence(hard_link_Sequence(cdnadb->rev->seq));
else
return cDNA_from_Sequence(hard_link_Sequence(cdnadb->forw->seq));
}
/* we need to get out the Sequence from seqdb */
seq = get_Sequence_from_SequenceDB(cdnadb->sdb,de);
if( seq == NULL ) {
warn("Cannot get entry for %s from cDNA db",de->name);
return NULL;
}
if( seq->type != SEQUENCE_DNA) {
warn("Sequence from %s data entry doesn't look like DNA. Forcing it to",de->name);
}
force_to_dna_Sequence(seq,1.0,NULL);
if( de->is_reversed == TRUE ) {
temp = reverse_complement_Sequence(seq);
free_Sequence(seq);
seq = temp;
}
return cDNA_from_Sequence(seq);
}
Genomic * get_Genomic_from_GenomicDB(GenomicDB * gendb,DataEntry * de)
{
Sequence * seq;
Sequence * temp;
/* we need to get out the Sequence from seqdb */
if( gendb == NULL || de == NULL ) {
warn("Cannot get a genomic sequence from NULL objects. Ugh!");
return NULL;
}
if( gendb->is_single_seq) {
if( de->is_reversed == TRUE )
return hard_link_Genomic(gendb->revsingle);
else
return hard_link_Genomic(gendb->single);
}
seq = get_Sequence_from_SequenceDB(gendb->sdb,de);
if( seq == NULL ) {
warn("Cannot get entry for %s from Genomic db",de->name);
}
/* check dna status. We assumme someone knows what he is doing when he makes a genomic db!*/
if( seq->type != SEQUENCE_DNA) {
warn("Sequence from %s data entry doesn't look like DNA. Forcing it to",de->name);
}
force_to_dna_Sequence(seq,1.0,NULL);
if( de->is_reversed == TRUE ) {
temp = reverse_complement_Sequence(seq);
free_Sequence(seq);
seq = temp;
}
return Genomic_from_Sequence_Nheuristic(seq,gendb->length_of_N);
}
ComplexSequence * reload_cDNADB(ComplexSequence * last,cDNADB * cdnadb,int * return_status)
{
ComplexSequence * cs;
Sequence * seq,*temp;
/** free Complex Sequence **/
if ( last != NULL ) {
free_ComplexSequence(last);
}
if( cdnadb->forward_only == TRUE) {
temp = reload_SequenceDB(NULL,cdnadb->sdb,return_status);
if ( *return_status != DB_RETURN_OK ) {
return NULL;
}
cs = new_ComplexSequence(temp,cdnadb->cses);
return cs;
}
if( cdnadb->is_single_seq == TRUE ) {
if( cdnadb->done_forward == TRUE ) {
*return_status = DB_RETURN_OK;
cdnadb->done_forward = FALSE;
return hard_link_ComplexSequence(cdnadb->rev);
} else {
*return_status = DB_RETURN_END;
return NULL;
}
}
/** standard database **/
if( cdnadb->done_forward == TRUE ) {
if( cdnadb->current == NULL ) {
warn("A bad internal cDNA db error - unable to find current sequence in db reload");
*return_status = DB_RETURN_ERROR;
return NULL;
}
temp = reverse_complement_Sequence(cdnadb->current);
if( temp == NULL ) {
warn("A bad internal cDNA db error - unable to reverse complements current");
*return_status = DB_RETURN_ERROR;
return NULL;
}
cs = new_ComplexSequence(temp,cdnadb->cses);
if( cs == NULL ) {
warn("A bad internal cDNA db error - unable to make complex sequence in db reload");
*return_status = DB_RETURN_ERROR;
return NULL;
}
free_Sequence(temp);
cdnadb->done_forward = FALSE;
return cs;
}
/* otherwise we have to get a new sequence */
seq = reload_SequenceDB(NULL,cdnadb->sdb,return_status);
if( seq == NULL || *return_status == DB_RETURN_ERROR || *return_status == DB_RETURN_END ) {
return NULL; /** error already reported **/
}
uppercase_Sequence(seq);
if( force_to_dna_Sequence(seq,cdnadb->error_tol,NULL) == FALSE ) {
if( cdnadb->error_handling == CDNADB_READ_THROUGH ) {
warn("Unable to map %s sequence to a cDNA sequence, but ignoring that for the moment...",seq->name);
free_Sequence(seq);
return reload_cDNADB(NULL,cdnadb,return_status);
} else {
warn("Unable to map %s sequence to a cDNA sequence. Failing",seq->name);
*return_status = DB_RETURN_ERROR;
return NULL;
}
}
cs = new_ComplexSequence(seq,cdnadb->cses);
if( cs == NULL ) {
if( cdnadb->error_handling == CDNADB_READ_THROUGH ) {
warn("Unable to map %s sequence to a cDNA sequence, but ignoring that for the moment...",seq->name);
free_Sequence(seq);
return reload_cDNADB(NULL,cdnadb,return_status);
} else {
warn("Unable to map %s sequence to a cDNA sequence. Failing",seq->name);
*return_status = DB_RETURN_ERROR;
return NULL;
}
}
cdnadb->current = free_Sequence(cdnadb->current);
cdnadb->current = seq;
cdnadb->done_forward= TRUE;
return cs;
}
DnaProfileSet * DnaProfileSet_from_leaf_node(Sequence * one,DnaProfileSet * two,DnaProfileEnginePara * dpep)
{
DnaProfileSet * out;
DnaProfile * dnap;
DnaProfile * dnapr;
DnaProfileMatchPairSet * dpmps;
Sequence * rev;
SeqAlign * sa;
DnaProfile * new_dnap;
int i;
int j;
dpmps = DnaProfileMatchPairSet_alloc_std();
out = DnaProfileSet_alloc_std();
rev = reverse_complement_Sequence(one);
dnap = naive_DnaProfile_from_Sequence(one,dpep->seq_id,dpep->m2i,dpep->m2d,dpep->i2i,dpep->d2d);
dnapr = naive_DnaProfile_from_Sequence(rev,dpep->seq_id,dpep->m2i,dpep->m2d,dpep->i2i,dpep->d2d);
fold_RandomModel_DnaProfile(dnap,dpep->rm);
fold_RandomModel_DnaProfile(dnapr,dpep->rm);
for(i=0; i<two->len; i++) {
fprintf(stderr,"Processing %d\n",i);
add_DnaProfileMatchPairSet(dpmps,DnaProfileMatchPair_from_DnaProfile(dnap,two->dnap[i],dpep));
add_DnaProfileMatchPairSet(dpmps,DnaProfileMatchPair_from_DnaProfile(dnapr,two->dnap[i],dpep));
}
fprintf(stderr,"Sorting....\n");
sort_DnaProfileMatchPairSet_by_score(dpmps);
for(i=0; i<dpmps->len; i++) {
/* check this profile has not already been used */
/* not done yet */
if( dpmps->pair[i]->score < dpep->min_seq_prof ) {
fprintf(stderr,"Warning... rejecting match due to score %d vs %d\n",dpmps->pair[i]->score,dpep->min_seq_prof);
break;
}
sa = merged_SeqAlign(dpmps->pair[i]->query,dpmps->pair[i]->target,dpmps->pair[i]->alb);
new_dnap = naive_DnaProfile_from_SeqAlign(sa,dpep->pseudo,dpep->m2i,dpep->m2d,dpep->i2i,dpep->d2d);
/* need to log-odds dnap here */
fold_RandomModel_DnaProfile(new_dnap,dpep->rm);
add_DnaProfileSet(out,new_dnap);
}
fprintf(stderr,"Freeing DNA profiles...\n");
free_DnaProfile(dnap);
free_DnaProfile(dnapr);
fprintf(stderr,"Freeing sequences\n");
free_Sequence(rev);
return out;
}
DnaProfileSet * DnaProfileSet_from_leaf_leaf(Sequence * one,Sequence * two,DnaProfileEnginePara * dpep)
{
DnaProfileSet * out;
DnaMatrix * dm;
DnaProbMatrix * dmp;
PairwiseShortDna * psd;
LocalCisHitSet * set;
Sequence * two_rev;
DnaProfile * dp;
SeqAlign * sa;
Sequence * temp1;
Sequence * temp2;
char * temp_seq1;
char * temp_seq2;
int unmatched;
int seq1_i,seq2_i;
AlnColumn * alc;
int i;
two_rev = reverse_complement_Sequence(two);
dmp = DnaProbMatrix_from_match(0.65,NMaskType_BANNED);
assert(dmp);
flat_null_DnaProbMatrix(dmp);
dm = DnaMatrix_from_DnaProbMatrix(dmp);
show_DnaMatrix(dm,stderr);
psd = query_to_reverse_target(one,two,dm,0,one->len,0,two->len);
set = make_LocalCisHitSet(one,two,two_rev,psd->forward,psd->reverse,dpep->setpara,dpep->lchs,NULL,NULL,NULL,NULL,0,dpep->dpri);
temp_seq1 = calloc(one->len > two->len ? one->len : two->len,sizeof(char));
temp_seq2 = calloc(one->len > two->len ? one->len : two->len,sizeof(char));
out = DnaProfileSet_alloc_std();
for(i=0; i<set->len; i++) {
unmatched = 1;
sa = NULL;
/*
* Main loop over DBA style alignment. We need to make one
* DnaProfile per matching block, which are separated by unmatched
* blocks. Could potentially be no blocks.
*
* Extra annoyance provided by the "wrong" convention being used in
* DBA alignments, meaning that "inserts" label the "sequence" containing
* strand, not the non-sequence containing strand. Stupid, but dbadisplay
* uses this convention, so if we changed, would have to fix lots of exisiting
* code. Not ideal.
*
*/
for(alc=set->lch[i]->alb->start; alc != NULL; alc=alc->next) {
/* hitting an unmatched block */
if( unmatched == 0 && (strcmp(alc->alu[0]->text_label,"UM") == 0 ||
strcmp(alc->alu[0]->text_label,"UI") == 0 || strcmp(alc->alu[0]->text_label,"END") == 0) ) {
/* if we have an alignment, put it away now */
if( sa != NULL ) {
temp_seq1[seq1_i] = '\0';
temp_seq2[seq2_i] = '\0';
temp1 = Sequence_from_static_memory(one->name,temp_seq1);
temp2 = Sequence_from_static_memory(two->name,temp_seq2);
add_SeqAlign(sa,temp1);
add_SeqAlign(sa,temp2);
dp = naive_DnaProfile_from_SeqAlign(sa,0.15,0.1,0.1,0.8,0.8);
fold_RandomModel_DnaProfile(dp,dpep->rm);
add_DnaProfileSet(out,dp);
free_SeqAlign(sa); /* hard linked inside DP */
sa = NULL;
}
continue;
} else if( unmatched == 1 && (strstartcmp(alc->alu[0]->text_label,"MM") == 0 ||
strstartcmp(alc->alu[0]->text_label,"MI") == 0 ) ) {
unmatched = 0;
sa = SeqAlign_alloc_len(2);
seq1_i = 0;
seq2_i = 0;
}
/* only if we are in a matched block */
if( unmatched == 0 ) {
/* Bloody twisted DBA convention - Niclas has alot to answer for.
Evil stuff -- MI is on the wrong strand! */
if( strstartcmp(alc->alu[0]->text_label,"MI") == 0 ) {
/* means 0 has sequence, other has gap */
temp_seq1[seq1_i++] = one->seq[alc->alu[0]->end];
temp_seq2[seq2_i++] = '-';
} else if ( strstartcmp(alc->alu[1]->text_label,"MI") == 0 ) {
temp_seq1[seq1_i++] = '-';
temp_seq2[seq2_i++] = two->seq[alc->alu[1]->end];
} else if ( strstartcmp(alc->alu[0]->text_label,"MM") == 0 &&
strstartcmp(alc->alu[1]->text_label,"MM") == 0 ) {
temp_seq1[seq1_i++] = one->seq[alc->alu[0]->end];
temp_seq2[seq2_i++] = two->seq[alc->alu[1]->end];
} else {
warn("Impossible label pair reached in matched block local cis hit stuff, %s,%s",alc->alu[0]->text_label,alc->alu[1]->text_label);
}
}
}
}
free(temp_seq1);
free(temp_seq2);
free_PairwiseShortDna(psd);
free_LocalCisHitSet(set);
free_DnaMatrix(dm);
free_DnaProbMatrix(dmp);
return out;
}
int main(int argc,char ** argv)
{
int type = ALIGN_NORMAL;
DPRunImpl * dpri = NULL;
HitList * hl;
HitListOutputImpl * hloi;
Sequence * query;
Sequence * target;
Sequence * target_rev;
PairwiseShortDna * two;
LocalCisHitSet * set;
LocalCisHitSet * greedy_set;
LocalCisHitScore * lchs;
LocalCisHitSetPara * setpara;
MotifMatrixPara * mmp;
MotifMatrixScore * mms;
TransFactorMatchSet * tfms_query = NULL;
TransFactorMatchSet * tfms_target = NULL;
TransFactorMatchSet * tfms_target_rev = NULL;
int qstart = -1;
int qend = -1;
int tstart = -1;
int tend = -1;
int i;
char * temp;
DnaMatrix * dm;
DnaProbMatrix * dmp;
TransFactorBuildPara * tfbp;
TransFactorMatchPara * tfmp;
TransFactorSet * tfs;
char * motif_library = NULL;
int use_laurence = FALSE;
int use_ben = FALSE;
dmp = DnaProbMatrix_from_match(0.75,NMaskType_BANNED);
assert(dmp);
flat_null_DnaProbMatrix(dmp);
dm = DnaMatrix_from_DnaProbMatrix(dmp);
dpri = new_DPRunImpl_from_argv(&argc,argv);
hloi = new_HitListOutputImpl_from_argv(&argc,argv);
setpara = new_LocalCisHitSetPara_from_argv(&argc,argv);
mmp = new_MotifMatrixPara_from_argv(&argc,argv);
tfbp = new_TransFactorBuildPara_from_argv(&argc,argv);
tfmp = new_TransFactorMatchPara_from_argv(&argc,argv);
strip_out_integer_argument(&argc,argv,"s",&qstart);
strip_out_integer_argument(&argc,argv,"t",&qend);
strip_out_integer_argument(&argc,argv,"u",&tstart);
strip_out_integer_argument(&argc,argv,"v",&tend);
temp = strip_out_assigned_argument(&argc,argv,"motiflib");
if( temp != NULL ) {
motif_library = stringalloc(temp);
}
use_laurence = strip_out_boolean_argument(&argc,argv,"lr");
use_ben = strip_out_boolean_argument(&argc,argv,"ben");
temp = strip_out_assigned_argument(&argc,argv,"align");
if( temp != NULL ) {
if( strcmp(temp,"motif") == 0 ) {
type = ALIGN_MOTIF;
} else if ( strcmp(temp,"normal") == 0 ) {
type = ALIGN_NORMAL;
} else {
fatal("cannot recognise string %s as align type",temp);
}
}
strip_out_standard_options(&argc,argv,show_help,show_version);
if( argc != 3 ) {
show_help(stdout);
exit(12);
}
lchs = standard_LocalCisHitScore(NMaskType_VARIABLE);
query = read_fasta_file_Sequence(argv[1]);
target = read_fasta_file_Sequence(argv[2]);
for(i=0;i<query->len;i++) {
query->seq[i] = toupper(query->seq[i]);
}
assert(query != NULL);
assert(target != NULL);
target_rev = reverse_complement_Sequence(target);
mms = MotifMatrixScore_from_MotifMatrixPara(mmp);
if( type == ALIGN_MOTIF ) {
if( motif_library == NULL ) {
fatal("Wanted to align with motif but not motif library. Must use -motiflib");
}
if( use_laurence == TRUE ) {
tfs = read_laurence_TransFactorSet_file(motif_library);
} else if( use_ben == TRUE ) {
tfs = read_ben_IUPAC_TransFactorSet_file(motif_library);
} else {
tfs = read_TransFactorSet_file(motif_library);
}
build_TransFactorSet(tfs,tfbp);
tfms_query = calculate_TransFactorMatchSet(query,tfs,tfmp);
sort_by_start_TransFactorMatchSet(tfms_query);
tfms_target = calculate_TransFactorMatchSet(target,tfs,tfmp);
sort_by_start_TransFactorMatchSet(tfms_target);
tfms_target_rev = calculate_TransFactorMatchSet(target_rev,tfs,tfmp);
sort_by_start_TransFactorMatchSet(tfms_target);
fprintf(stdout,"Motif Set: %d in query and %d in target\n",tfms_query->len,tfms_target->len);
}
if( qstart == -1 ) {
qstart = 0;
}
if( qend == -1 ) {
qend = query->len;
}
if( tstart == -1 ) {
tstart = 0;
}
if( tend == -1 ) {
tend = target->len;
}
two = query_to_reverse_target(query,target,dm,qstart,qend,tstart,tend);
set = make_LocalCisHitSet(query,target,target_rev,two->forward,two->reverse,setpara,lchs,tfms_query,tfms_target,tfms_target_rev,mms,type == ALIGN_MOTIF ? 1 : 0,dpri);
greedy_set = greedy_weed_LocalCisHitSet(set,setpara);
hl = HitList_from_LocalCisHitSet(greedy_set);
show_HitList_HitListOutputImpl(hloi,hl,stdout);
return 0;
}
