Score logl_positive_selection(char * ref,char * diff,RandomModel * rm,CodonTable *ct,DnaProbMatrix * dm)
{
int i;
Score s = 0;
char ref_aa;
char diff_aa;
/* we have to assess this position having changed */
for(i=0;i<3;i++) {
s += Probability2Score(dm->prob[base_from_char(ref[i])][base_from_char(diff[i])]);
}
/* if the position has not changed, then we know it would have been selected */
ref_aa = aminoacid_from_seq(ct,ref);
diff_aa = aminoacid_from_seq(ct,diff);
if( ref_aa == diff_aa ) {
return s;
}
/* else we add the probability of seeing this amino acid*/
s += Probability2Score(rm->aminoacid[diff_aa-'A']);
return s;
}
Sequence * translate_swapped(Sequence * swapped)
{
CodonTable * ct;
int i,j;
Sequence * out;
out = Sequence_alloc();
out->name = stringalloc(swapped->name);
out->seq = calloc(1+swapped->len/3,sizeof(char));
ct = read_CodonTable_file("codon.table");
for(i=0,j=0;i<swapped->len;i+=3,j++) {
out->seq[j] = aminoacid_from_seq(ct,swapped->seq+i);
if( isupper(swapped->seq[i]) && isupper(swapped->seq[i+1]) &&
isupper(swapped->seq[i+2]) ) {
out->seq[j] = toupper(out->seq[j]);
} else{
out->seq[j] = tolower(out->seq[j]);
}
}
out->seq[j] = '\0';
return out;
}
Sequence * translate_Sequence(Sequence * dna,CodonTable * ct)
{
Sequence * out;
int i;
int j;
int len;
char * seq;
char * name;
char buffer[512];
if( is_dna_Sequence(dna) == FALSE) {
warn("Trying to make a translation from a non DNA sequence... type is [%s]",Sequence_type_to_string(dna->type));
return NULL;
}
len = dna->len/3 + 1;
seq = ckcalloc(len,sizeof(char));
sprintf(buffer,"%s.tr",dna->name == NULL ? "NoNameDNASeq" : dna->name);
name = stringalloc(buffer);
out = Sequence_from_dynamic_memory(name,seq);
for(i=0,j=0;i<dna->len-3;i+=3,j++) {
out->seq[j] = aminoacid_from_seq(ct,dna->seq+i);
}
out->seq[j] = '\0';
out->type = SEQUENCE_PROTEIN;
out->len = strlen(out->seq);
return out;
}
void show_PairBaseCodonModelScore(PairBaseCodonModelScore * sc,CodonTable * ct,FILE * ofp)
{
int i;
pairbase_type a;
pairbase_type b;
pairbase_type c;
int anchor_a;
int anchor_b;
int anchor_c;
int informant_a;
int informant_b;
int informant_c;
char seq1[4];
char seq2[4];
seq1[3] = seq2[3] = '\0';
for(i=0;i<PAIRBASE_CODON_LENGTH;i++) {
decompose_pairbase_codon(i,&a,&b,&c);
anchor_a = anchor_base_from_pairbase(a);
anchor_b = anchor_base_from_pairbase(b);
anchor_c = anchor_base_from_pairbase(c);
informant_a = informant_base_from_pairbase(a);
informant_b = informant_base_from_pairbase(b);
informant_c = informant_base_from_pairbase(c);
seq1[0] = char_for_base(anchor_a);
seq1[1] = char_for_base(anchor_b);
seq1[2] = char_for_base(anchor_c);
seq2[0] = char_for_base(informant_a);
seq2[1] = char_for_base(informant_b);
seq2[2] = char_for_base(informant_c);
fprintf(ofp,"%9d %s[%c] %s[%c] : %d\n",i,seq1,aminoacid_from_seq(ct,seq1),seq2,aminoacid_from_seq(ct,seq2),sc->codon[i]);
}
}
Score logl_negative_selection(char * ref,char * diff,ThreeStateUnit * unit,CodonTable * ct,DnaProbMatrix * dm)
{
int i;
Score s = 0;
char ref_aa;
char diff_aa;
/* we have to assess this position having changed */
for(i=0;i<3;i++) {
s += Probability2Score(dm->prob[base_from_char(ref[i])][base_from_char(diff[i])]);
}
/* if the position has not changed, then we know it could not have been selected */
ref_aa = aminoacid_from_seq(ct,ref);
diff_aa = aminoacid_from_seq(ct,diff);
if( ref_aa == diff_aa ) {
return s;
}
/* else we add the difference in probability between the two amino acids */
/*
fprintf(stdout,"%c vs %c has %d plays %d for total of %d\n",ref_aa,diff_aa,
Probability2Score(unit->match_emission[ref_aa-'A']),
Probability2Score(unit->match_emission[diff_aa-'A']),
Probability2Score(unit->match_emission[diff_aa-'A']) - Probability2Score(unit->match_emission[ref_aa-'A'])
);
*/
s += Probability2Score(unit->match_emission[diff_aa-'A']) - Probability2Score(unit->match_emission[ref_aa-'A']);
return s;
}
Protein * get_Protein_from_Translation(Translation * ts,CodonTable * ct)
{
cDNA * cd;
int i,j;
Sequence * seq;
char buffer[64];
assert(ts);
assert(ct);
/* fprintf(stderr,"Codon table is %d\n",ct);*/
if( ts->protein != NULL)
return ts->protein;
if( ts->parent == NULL ) {
warn("Cannot get Protein from translation as no parent!");
return NULL;
}
cd = get_cDNA_from_Transcript(ts->parent);
if( cd == NULL ) {
warn("Cannot make translation as can't get transcript!");
return NULL;
}
if( cd->baseseq == NULL ) {
warn("A bad error - a non NULL cDNA with a null sequence object. No translation here!");
return NULL;
}
if( cd->baseseq->len == 0 ) {
warn("Attempting to translate a zero length cDNA. Yikes!");
return NULL;
}
seq = Sequence_alloc();
sprintf(buffer,"%s.tr",cDNA_name(cd));
seq->name = stringalloc(buffer);
seq->seq = ckcalloc((cd->baseseq->len/3) + 2,sizeof(char));
seq->type = SEQUENCE_PROTEIN;
if( cd->baseseq->len%3 != 0 ) {
warn("Problem in making translation, cDNA is not mod3! - length is %d - transcript id %s",cd->baseseq->len,seq->name);
}
for(i=0,j=0;i<cd->baseseq->len;i+=3,j++) {
if( is_stop_codon(codon_from_seq(cd->baseseq->seq+i),ct) == TRUE ) {
if( i+3 >= cd->baseseq->len )
break;
else {
warn("Got a stop codon in the middle of a translation at postion [%d]. Yuk!",i);
seq->seq[j] = '*';
}
} else {
seq->seq[j] = aminoacid_from_seq(ct,cd->baseseq->seq+i);
}
}
seq->seq[j]='\0';
make_len_type_Sequence(seq);
/*write_fasta_Sequence(seq,stdout);*/
seq->type = SEQUENCE_PROTEIN;
ts->protein = Protein_from_Sequence(seq);
return ts->protein;
}
void debug_genomewise(AlnBlock * alb,GenomeEvidenceSet * ges,CodonTable * ct,Sequence * gen,FILE * ofp)
{
AlnColumn *alc;
int cstart;
for(alc=alb->start;alc != NULL;alc = alc->next ) {
fprintf(ofp,"%4d %12s %12s [%3d][%5d %5d] ",alc->alu[1]->score[0],alc->alu[0]->text_label,alc->alu[1]->text_label,alc->alu[0]->start,alc->alu[1]->start+1,alc->alu[1]->end);
if( strstartcmp(alc->alu[1]->text_label,"CODON") == 0 ) {
cstart = alc->alu[1]->start+1;
fprintf(ofp,"%c%c%c %c\n",gen->seq[cstart],gen->seq[cstart+1],gen->seq[cstart+2],aminoacid_from_seq(ct,gen->seq+cstart));
} else {
fprintf(ofp,"\n");
}
}
}
boolean protdna_btc_display(AlnBlock * alb,char * protsequence,char * protname_in,int protoff,Sequence * dna,CodonTable * ct,int name,int main,btCanvas * btc,char (*match_central_line)(char,int,char),boolean multalign)
{
AlnColumn * alc;
AlnColumn * alc_temp,*alc_endscore;
int a_phase, d_phase;
int intron_number = 1;
int aln_score;
int aln_num = 1;
btPasteArea * btp;
char tempbuf[2];
char protname[60];
char dnaname[60];
char dnatemp[4];
char protc;
char transc;
boolean is_reversed = FALSE;
boolean issplit;
if( strlen(protname_in) > name ) {
info("Name %s is longer than allowed name block (%d). Truncating\n",protname_in,name);
strncpy(protname,protname_in,name);
protname[name] = '\0';
} else {
strcpy(protname,protname_in);
}
if( strlen(dna->name) > name ) {
info("Name %s is longer than allowed name block (%d). Truncating\n",dna->name,name);
strncpy(dnaname,dna->name,name);
dnaname[name] = '\0';
} else {
strcpy(dnaname,dna->name);
}
if( dna->offset > dna->end ) {
is_reversed = TRUE;
}
for(alc=alb->start;alc != NULL;) {
if ( strcmp(alc->alu[1]->text_label,"END") == 0 )
break; /* end of alignment */
for(;alc != NULL && is_random_AlnColumn_genewise(alc) == TRUE;alc = alc->next)
;
if( alc == NULL)
break; /* end of alignment */
if( multalign == TRUE ) {
/* get the end score */
for(aln_score = 0,alc_endscore=alc;alc_endscore->next != NULL;alc_endscore = alc_endscore->next) {
if( is_random_AlnColumn_genewise(alc_endscore) == TRUE)
break;
aln_score += alc_endscore->alu[0]->score[0];
}
/*aln_score += alc_endscore->alu[0]->score[0];*/
write_alignment_separator(btc,aln_num++,aln_score);
}
while( alc != NULL ) {
write_name_start_stuff(btc,protname,protoff,dnaname,dna,name,alc);
for(; alc != NULL;alc=alc->next ) {
if( is_random_AlnColumn_genewise(alc) == TRUE )
break;
if( strcmp(alc->alu[1]->text_label,"INSERT") == 0 ) {
if( can_get_paste_area_btCanvas(btc,1) == FALSE)
break; /* back to upper for, to place names and starts */
btp = get_paste_area_btCanvas(btc,1);
paste_char_btPasteArea(btp,0,0,protsequence[alc->alu[0]->start+1],0);
paste_char_btPasteArea(btp,0,2,'-',0);
free_btPasteArea(btp);
} else if ( strcmp(alc->alu[1]->text_label,"SEQUENCE_INSERTION") == 0 ||
strcmp(alc->alu[1]->text_label,"SEQUENCE_DELETION") == 0 ) {
if( can_get_paste_area_btCanvas(btc,1) == FALSE)
break; /* back to upper for, to place names and starts */
btp = get_paste_area_btCanvas(btc,1);
if( strcmp(alc->alu[0]->text_label,"INSERT_STATE")== 0 ) {
paste_char_btPasteArea(btp,0,0,'-',0);
}
else {
paste_char_btPasteArea(btp,0,0,protsequence[alc->alu[0]->end],0);
}
sprintf(tempbuf,"%d",alc->alu[1]->end - alc->alu[1]->start);
paste_char_btPasteArea(btp,0,3,tempbuf[0],0);
paste_char_btPasteArea(btp,0,2,'!',0);
free_btPasteArea(btp);
} else if (strcmp(alc->alu[1]->text_label,"END") == 0 && strcmp(alc->alu[0]->text_label,"END") == 0) {
break; /* end of alignment */
} else if ( strcmp(alc->alu[1]->text_label,"RANDOM_SEQUENCE") == 0 ) {
break;
} else if( strcmp(alc->alu[1]->text_label,"CODON") == 0 ) {
if( can_get_paste_area_btCanvas(btc,1) == FALSE)
break; /* back to upper for, to place names and starts */
btp = get_paste_area_btCanvas(btc,1);
if( strcmp(alc->alu[0]->text_label,"INSERT_STATE")== 0 ) {
write_codon_match(btp,'-',' ',alc->alu[1]->start+1,aminoacid_from_seq(ct,dna->seq+alc->alu[1]->start+1),dna->seq+alc->alu[1]->start+1);
}
else {
write_codon_match(btp,protsequence[alc->alu[0]->end],(*match_central_line)(protsequence[alc->alu[0]->end],alc->alu[0]->score[0],aminoacid_from_seq(ct,dna->seq+alc->alu[1]->start+1)),alc->alu[1]->start+1,aminoacid_from_seq(ct,dna->seq+alc->alu[1]->start+1),dna->seq+alc->alu[1]->start+1);
}
free_btPasteArea(btp);
continue;
} else if ( strstartcmp(alc->alu[1]->text_label,"5SS") == 0 ) {
/*
* intron stuff. Figure out the start and end,
* then place the 5'SS Central and End.
*
* If we can't fit in the intron, loop over
* in this region before returning to higher loop.
*
*/
if( strcmp(alc->alu[1]->text_label,"5SS_PHASE_0") == 0 ) {
d_phase = 0;
} else if ( strcmp(alc->alu[1]->text_label,"5SS_PHASE_1") == 0 ) {
d_phase = 1;
} else if ( strcmp(alc->alu[1]->text_label,"5SS_PHASE_2") == 0 ) {
d_phase = 2;
} else {
warn("No no no. You have a non 0,1,2 phase intron (god knows how!). Not displaying it %s",alc->alu[1]->text_label);
advance_line_btCanvas(btc);
return FALSE;
}
alc_temp = alc->next;
if( strcmp(alc_temp->alu[1]->text_label,"CENTRAL_INTRON") != 0 ) {
warn("Bad news. I have found a 5SS in your alignment, but it is not followed by a central intron node. Don't like it!");
advance_line_btCanvas(btc);
return FALSE;
}
for(alc_temp = alc_temp->next ;alc_temp != NULL && strstartcmp(alc_temp->alu[1]->text_label,"3SS") != 0;alc_temp = alc_temp->next)
;
if( alc_temp == NULL ) {
warn("Got to the end of the alignment in the middle of an intron from %s. Weird!",alc->alu[1]->text_label);
advance_line_btCanvas(btc);
return FALSE;
}
if( strcmp(alc_temp->alu[1]->text_label,"3SS_PHASE_0") == 0 ) {
a_phase = 0;
} else if ( strcmp(alc_temp->alu[1]->text_label,"3SS_PHASE_1") == 0 ) {
a_phase = 1;
} else if ( strcmp(alc_temp->alu[1]->text_label,"3SS_PHASE_2") == 0 ) {
a_phase = 2;
} else {
warn("No no no. You have a non 0,1,2 phase intron (god knows how!). Not displaying it %s",alc_temp->alu[1]->text_label);
advance_line_btCanvas(btc);
return FALSE;
}
/*
* At this point we have alc on 5SS alc_temp on 3SS.
*
* Check to see if we can place 5SS and Central intron piece
* on the line, if not advance.
*
*/
if( can_get_paste_area_btCanvas(btc,d_phase+7+13) == FALSE) {
advance_line_btCanvas(btc);
write_name_start_stuff(btc,protname,protoff,dnaname,dna,name,alc);
}
/*** ok, if we can't get it now then we are f****d ***/
if( can_get_paste_area_btCanvas(btc,d_phase+7+13) == FALSE) {
warn("You have specified a length of your main canvas too small. I need at least 23 characters long.");
advance_line_btCanvas(btc);
return FALSE;
}
btp = get_paste_area_btCanvas(btc,d_phase+7);
/* ? split phase */
if( a_phase == 0 || (a_phase != d_phase ) ) {
protc = ' ';
transc = ' ';
dnatemp[0]= '\0';
issplit = FALSE;
} else {
if( strcmp(alc_temp->alu[0]->text_label,"INSERT_STATE")== 0 ) {
protc = '-';
} else {
protc = protsequence[alc->alu[0]->start+1];
}
dnatemp[0] = tolower((int)dna->seq[alc->alu[1]->start+1]);
if( d_phase == 2) {
dnatemp[1] = tolower((int)dna->seq[alc->alu[1]->start+2]);
} else {
dnatemp[1] = tolower((int)dna->seq[alc_temp->alu[1]->end-1]);
}
dnatemp[2] = tolower((int)dna->seq[alc_temp->alu[1]->end]);
dnatemp[3] = '\0';
transc = aminoacid_from_seq(ct,dnatemp);
issplit = TRUE;
}
write_5intron_match(btp,d_phase,7,dna->seq+alc->alu[1]->start+1);
free_btPasteArea(btp);
btp = get_paste_area_btCanvas(btc,13);
if( is_reversed == FALSE )
write_intron_desc(btp,alc->alu[1]->start+1+d_phase+dna->offset,alc_temp->alu[1]->start+3+dna->offset,intron_number++,issplit,protc,transc,dnatemp);
else
write_intron_desc(btp,dna->offset - (alc->alu[1]->start+d_phase+1),dna->offset - (alc_temp->alu[1]->start+3),intron_number++,issplit,protc,transc,dnatemp);
free_btPasteArea(btp);
/*
* written the start of the intron, now to deal with the
* acceptor. We need to loop here, because we might go over the
* line length.
*/
alc = alc->next->next; /*** move alc forward two columns ***/
while( alc != alc_temp ) {
for(; alc != alc_temp;alc = alc->next) { /** alc_temp is 3SS **/
if( strcmp(alc->alu[1]->text_label,"PYRIMIDINE_TRACT") == 0 ) {
if( can_get_paste_area_btCanvas(btc,1) == FALSE )
break;
btp = get_paste_area_btCanvas(btc,1);
paste_char_btPasteArea(btp,0,3,dna->seq[alc->alu[1]->start+1],0);
paste_char_btPasteArea(btp,0,4,'+',0);
free_btPasteArea(btp);
} else if( strcmp(alc->alu[1]->text_label,"SPACER") == 0 ) {
if( can_get_paste_area_btCanvas(btc,1) == FALSE )
break;
btp = get_paste_area_btCanvas(btc,1);
paste_char_btPasteArea(btp,0,3,dna->seq[alc->alu[1]->start+1],0);
free_btPasteArea(btp);
} else {
warn("Sorry, don't know how to print %s. Skipping...",alc->alu[1]->text_label);
}
}
/** end for for loop **/
if ( alc == alc_temp ) {
break;
}
/*** run out of space ***/
advance_line_btCanvas(btc);
write_name_start_stuff(btc,protname,protoff,dnaname,dna,name,alc);
} /** end of while still in central->3SS **/
/*
* Now do 3SS
*
*/
if( can_get_paste_area_btCanvas(btc,a_phase == 0 ? 3 : 3- a_phase + 3) == FALSE ) {
advance_line_btCanvas(btc);
write_name_start_stuff(btc,protname,protoff,dnaname,dna,name,alc);
}
if( a_phase != 0 ) {
btp = get_paste_area_btCanvas(btc,3 - a_phase + 3);
write_3intron_match(btp,a_phase,3,dna->seq + alc->alu[1]->start+1);
free_btPasteArea(btp);
} else {
btp = get_paste_area_btCanvas(btc,3);
write_3intron_match(btp,a_phase,3,dna->seq + alc->alu[1]->start+1);
free_btPasteArea(btp);
}
/*
* Finished with intron !!!
*/
} else {
warn("Sorry, could not print the alignment %s:%s column",alc->alu[0]->text_label,alc->alu[1]->text_label);
}
} /*** in this loop ***/
advance_line_btCanvas(btc);
if( alc == NULL)
break;
if ( is_random_AlnColumn_genewise(alc) == TRUE)
break;
} /* end of while over alignments */
} /* end of foreach alignment */
/*** end of print ! **/
return TRUE;
}
void show_verbose_evo(AlnBlock * alb,ThreeStateModel * tsm,Sequence * ref,Sequence * diff,CodonTable * ct,FILE * ofp)
{
AlnColumn * alc;
Protein * hmmp;
Sequence * ref_trans;
Sequence * diff_trans;
DnaProbMatrix * negative_dm;
DnaProbMatrix * pseudo_dm;
int i;
int count = 0;
double est_mutation = 0.0;
int dna_offset;
Score total_pseudo = 0;
Score total_neg = 0;
Score pseudo = 0;
Score neg = 0;
int count_ref_positive = 0;
int count_ref_negative = 0;
int count_ref_negative_0_5 = 0;
int count_ref_negative_5_10 = 0;
int count_ref_negative_10_15 = 0;
int syn_sites = 0;
int nonsyn_sites = 0;
int syn_changes = 0;
int nonsyn_changes = 0;
int diff_score;
char diff_aa;
char ref_aa;
int score_ratio = 0;
Score score_neg_5 = Probability2Score(Bits2Probability(-5.0));
Score score_neg_10 = Probability2Score(Bits2Probability(-10.0));
int k;
for(i=0;i<ref->len;i+=3) {
/* if this has changed, then it is definitely non syn */
if( aminoacid_from_seq(ct,ref->seq+i) != aminoacid_from_seq(ct,diff->seq+i)) {
for(k=0;k<3;k++) {
if( ref->seq[i+k] != diff->seq[i+k] ) {
nonsyn_changes++;
}
}
} else {
/* could still be syn change */
for(k=0;k<3;k++) {
if( ref->seq[i+k] != diff->seq[i+k] ) {
syn_changes++;
}
}
}
/* calculate the sites. There is always 2 non syn sites */
nonsyn_sites += 2;
if( four_fold_sites_CodonTable(ct,ref->seq+i) > 0 ) {
syn_sites++;
} else {
nonsyn_sites += 1;
}
}
for(i=0;i<ref->len;i++) {
if( ref->seq[i] != diff->seq[i] ) {
count++;
}
}
est_mutation = (double)count / (double)ref->len;
pseudo_dm = DnaProbMatrix_from_match(1.0 - est_mutation,NMaskType_BANNED);
negative_dm = DnaProbMatrix_from_match(1.0 - (est_mutation*2),NMaskType_BANNED);
ref_trans = translate_Sequence(ref,ct);
diff_trans = translate_Sequence(diff,ct);
hmmp = pseudo_Protein_from_ThreeStateModel(tsm);
for(alc=alb->start;alc != NULL;alc = alc->next) {
/* fprintf(stdout,"In position %s\n",alc->alu[0]->text_label); */
if( strcmp(alc->alu[0]->text_label,"SEQUENCE") == 0 &&
strcmp(alc->alu[1]->text_label,"SEQUENCE") == 0 ) {
dna_offset = alc->alu[1]->end*3;
pseudo = logl_pseudogene(ref->seq+dna_offset,diff->seq+dna_offset,pseudo_dm);
neg = logl_negative_selection(ref->seq+dna_offset,diff->seq+dna_offset,tsm->unit[alc->alu[0]->end],ct,
pseudo_dm);
/*
fprintf(ofp,"Position %d [%c], vs %d [%c,%c] Scores Negative %d, Pseudo %d\n",
alc->alu[0]->end,hmmp->baseseq->seq[alc->alu[0]->end],
alc->alu[1]->end,ref_trans->seq[alc->alu[1]->end],diff_trans->seq[alc->alu[1]->end],
neg,
pseudo
);
*/
ref_aa = ref_trans->seq[alc->alu[1]->end];
diff_aa = diff_trans->seq[alc->alu[1]->end];
if( ref_aa != diff_aa ) {
score_ratio += Probability2Score(tsm->unit[alc->alu[0]->end]->match_emission[ref_aa-'A']) - Probability2Score(tsm->unit[alc->alu[0]->end]->match_emission[diff_aa-'A']);
diff_score = Probability2Score(tsm->unit[alc->alu[0]->end]->match_emission[ref_aa-'A']) - Probability2Score(tsm->unit[alc->alu[0]->end]->match_emission[diff_aa-'A']);
if( diff_score < 0) {
count_ref_negative++;
if( diff_score > score_neg_5 ) {
count_ref_negative_0_5++;
} else if ( diff_score > score_neg_10 ) {
count_ref_negative_5_10++;
} else {
count_ref_negative_10_15++;
}
} else {
count_ref_positive++;
}
}
total_pseudo += pseudo;
total_neg += neg;
}
}
fprintf(ofp,"%s\t%s\t%.2f\t%d\t%d\t%d\t%d\t%d\n",ref->name,hmmp->baseseq->name,Score2Bits(score_ratio),
count_ref_positive,count_ref_negative,
count_ref_negative_0_5,
count_ref_negative_5_10,
count_ref_negative_10_15);
/*
fprintf(ofp,"%s,%s Total Pseudo %d vs Negative %d, Ratio %.4f Positive %d Negative %d Score %.2f Syn %d Changes %d NonSyn %d Changes %d\n",ref->name,hmmp->baseseq->name,total_pseudo,total_neg,Score2Bits(total_neg-total_pseudo),count_ref_positive,count_ref_negative,Score2Bits(score_ratio),syn_sites,syn_changes,nonsyn_sites,nonsyn_changes);
*/
free_Protein(hmmp);
}
void show_score_sequence(AlnBlock * alb,PairBaseSeq * pbs,PairBaseModelScore * m,FILE * ofp)
{
AlnColumn * alc;
char seq1[20];
char seq2[20];
int match_score = 0;
for(alc=alb->start; alc != NULL; alc=alc->next) {
if( strcmp(alc->alu[1]->text_label,"CODON") == 0 ) {
seq1[0] = char_for_base(anchor_base_from_pairbase(pbs->seq[alc->alu[1]->start+1]));
seq1[1] = char_for_base(anchor_base_from_pairbase(pbs->seq[alc->alu[1]->start+2]));
seq1[2] = char_for_base(anchor_base_from_pairbase(pbs->seq[alc->alu[1]->start+3]));
seq2[0] = char_for_base(informant_base_from_pairbase(pbs->seq[alc->alu[1]->start+1]));
seq2[1] = char_for_base(informant_base_from_pairbase(pbs->seq[alc->alu[1]->start+2]));
seq2[2] = char_for_base(informant_base_from_pairbase(pbs->seq[alc->alu[1]->start+3]));
seq1[3] = '\0';
seq2[3] = '\0';
match_score = m->base[pbs->seq[alc->alu[1]->start+1]];
match_score += m->base[pbs->seq[alc->alu[1]->start+2]];
match_score += m->base[pbs->seq[alc->alu[1]->start+3]];
fprintf(ofp,"%s %5d %5d %s [%c] vs %s [%c] %-.2f %-.2f\n",alc->alu[1]->text_label,alc->alu[0]->start+1,alc->alu[1]->start+1,seq1,aminoacid_from_seq(ct,seq1),seq2,aminoacid_from_seq(ct,seq2),Score2Bits(alc->alu[0]->score[0]),Score2Bits(match_score));
}
if( strstr(alc->alu[1]->text_label,"SS") != NULL ) {
seq1[0] = char_for_base(anchor_base_from_pairbase(pbs->seq[alc->alu[1]->start-3]));
seq1[1] = char_for_base(anchor_base_from_pairbase(pbs->seq[alc->alu[1]->start-2]));
seq1[2] = char_for_base(anchor_base_from_pairbase(pbs->seq[alc->alu[1]->start-1]));
seq1[3] = char_for_base(anchor_base_from_pairbase(pbs->seq[alc->alu[1]->start]));
seq1[4] = char_for_base(anchor_base_from_pairbase(pbs->seq[alc->alu[1]->start+1]));
seq1[5] = char_for_base(anchor_base_from_pairbase(pbs->seq[alc->alu[1]->start+2]));
seq1[6] = char_for_base(anchor_base_from_pairbase(pbs->seq[alc->alu[1]->start+3]));
seq1[7] = char_for_base(anchor_base_from_pairbase(pbs->seq[alc->alu[1]->start+4]));
seq1[8] = char_for_base(anchor_base_from_pairbase(pbs->seq[alc->alu[1]->start+5]));
seq1[9] = char_for_base(anchor_base_from_pairbase(pbs->seq[alc->alu[1]->start+6]));
seq1[10] = char_for_base(anchor_base_from_pairbase(pbs->seq[alc->alu[1]->start+7]));
seq2[0] = char_for_base(informant_base_from_pairbase(pbs->seq[alc->alu[1]->start-3]));
seq2[1] = char_for_base(informant_base_from_pairbase(pbs->seq[alc->alu[1]->start-2]));
seq2[2] = char_for_base(informant_base_from_pairbase(pbs->seq[alc->alu[1]->start-1]));
seq2[3] = char_for_base(informant_base_from_pairbase(pbs->seq[alc->alu[1]->start]));
seq2[4] = char_for_base(informant_base_from_pairbase(pbs->seq[alc->alu[1]->start+1]));
seq2[5] = char_for_base(informant_base_from_pairbase(pbs->seq[alc->alu[1]->start+2]));
seq2[6] = char_for_base(informant_base_from_pairbase(pbs->seq[alc->alu[1]->start+3]));
seq2[7] = char_for_base(informant_base_from_pairbase(pbs->seq[alc->alu[1]->start+4]));
seq2[8] = char_for_base(informant_base_from_pairbase(pbs->seq[alc->alu[1]->start+5]));
seq2[9] = char_for_base(informant_base_from_pairbase(pbs->seq[alc->alu[1]->start+6]));
seq2[10] = char_for_base(informant_base_from_pairbase(pbs->seq[alc->alu[1]->start+7]));
seq1[11] = '\0';
seq2[11] = '\0';
fprintf(ofp,"%12s %5d %5d %.2f\n",alc->alu[1]->text_label,alc->alu[0]->start+1,alc->alu[1]->start+1,Score2Bits(alc->alu[0]->score[0]));
fprintf(ofp," %s\n %s\n",seq1,seq2);
}
}
}
