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hits.cc
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/*
SWIPE
Smith-Waterman database searches with Inter-sequence Parallel Execution
Copyright (C) 2008-2014 Torbjorn Rognes, University of Oslo,
Oslo University Hospital and Sencel Bioinformatics AS
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as
published by the Free Software Foundation, either version 3 of the
License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Affero General Public License for more details.
You should have received a copy of the GNU Affero General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
Contact: Torbjorn Rognes <[email protected]>,
Department of Informatics, University of Oslo,
PO Box 1080 Blindern, NO-0316 Oslo, Norway
*/
#include "swipe.h"
long keephits;
long scorethreshold;
long upperscorethreshold;
int hits_count;
long init_threshold;
long obvious;
long opt_descriptions;
long opt_alignments;
/* parameters for bit scores and expect values */
long stats_available = 0;
double alpha;
double beta;
double lambda;
double K;
double H;
double Kmn = 0;
double logK;
double lambda_d_log2;
double logK_d_log2;
struct hits_entry
{
char * alignment;
char * dseq;
char * header_address;
long seqno;
long qstrand;
long qframe;
long dstrand;
long dframe;
long dlen;
long dlennt;
long score;
long score_align;
long align_hint;
long bestq;
long align_q_start;
long align_q_end;
long align_d_start;
long align_d_end;
long header_length;
} * hits_list;
pthread_mutex_t hitsmutex = PTHREAD_MUTEX_INITIALIZER;
int hits_compare(const void * a, const void * b)
{
struct hits_entry * ap = hits_list + *((long *) a);
struct hits_entry * bp = hits_list + *((long *) b);
if ( (*((long*)a) >= opt_alignments) < (*((long*)b) >= opt_alignments) )
{
return -1;
}
else if ( (*((long*)a) >= opt_alignments) > (*((long*)b) >= opt_alignments) )
{
return +1;
}
else if (ap->qstrand < bp->qstrand)
{
return -1;
}
else if (ap->qstrand > bp->qstrand)
{
return +1;
}
else if (ap->qframe < bp->qframe)
{
return -1;
}
else if (ap->qframe > bp->qframe)
{
return +1;
}
else if (ap->seqno < bp->seqno)
{
return -1;
}
else if (ap->seqno > bp->seqno)
{
return +1;
}
else if (ap->dstrand < bp->dstrand)
{
return -1;
}
else if (ap->dstrand > bp->dstrand)
{
return +1;
}
else if (ap->dframe < bp->dframe)
{
return -1;
}
else if (ap->dframe > bp->dframe)
{
return +1;
}
return 0;
}
long * hits_sort()
{
long * hits_sorted = (long *) xmalloc(hits_count * sizeof(long));
for(long i=0; i<hits_count; i++)
hits_sorted[i] = i;
qsort(hits_sorted, hits_count, sizeof(long), hits_compare);
#if 0
fprintf(out, "Hits sorted:\n");
fprintf(out, "Hitno Order Vol Seqno S F S F Score\n");
for(long i=0; i<hits_count; i++)
{
struct hits_entry * h = hits_list + hits_sorted[i];
fprintf(out, "%5ld %5ld %3ld %8ld %ld %ld %ld %ld %5ld\n",
h - hits_list + 1,
i+1,
db_getvolume(h->seqno),
h->seqno, h->qstrand, h->qframe, h->dstrand, h->dframe, h->score);
}
fprintf(out, "\n");
#endif
return hits_sorted;
}
void hits_enter(long seqno, long score, long qstrand, long qframe,
long dstrand, long dframe, long align_hint, long bestq)
{
// show_progress();
// fprintf(out, "Entering score %u from sequence no %u.\n", score, seqno);
// find correct place
pthread_mutex_lock(&hitsmutex);
if (score > upperscorethreshold)
obvious++;
if (score >= init_threshold)
totalhits++;
if ((score < scorethreshold) || (score > upperscorethreshold))
{
pthread_mutex_unlock(&hitsmutex);
return;
}
long place = hits_count;
while ((place > 0) && ((score > hits_list[place-1].score) ||
((score == hits_list[place-1].score) &&
(seqno > hits_list[place-1].seqno))))
place--;
// move entries down
long move = (hits_count < keephits ? hits_count : keephits - 1) - place;
// fprintf(out, "Inserting at place %d, moving %d.\n", place, move);
for (long j=move; j>0; j--)
hits_list[place+j] = hits_list[place+j-1];
// fill new entry
if (place < keephits)
{
hits_list[place].seqno = seqno;
hits_list[place].qstrand = qstrand;
hits_list[place].qframe = qframe;
hits_list[place].dstrand = dstrand;
hits_list[place].dframe = dframe;
hits_list[place].score = score;
hits_list[place].align_hint = align_hint;
hits_list[place].bestq = bestq;
if (hits_count < keephits)
hits_count++;
}
if (hits_count == keephits)
scorethreshold = hits_list[keephits-1].score;
pthread_mutex_unlock(&hitsmutex);
}
long hits_getcount()
{
return hits_count;
}
void hits_gethit(long i, long * seqno, long * score,
long * qstrand, long * qframe,
long * dstrand, long * dframe)
{
struct hits_entry * h = hits_list + i;
*seqno = h->seqno;
*score = h->score;
*qstrand = h->qstrand;
*qframe = h->qframe;
*dstrand = h->dstrand;
*dframe = h->dframe;
}
void hits_enter_seq(long i, char* seq, long seq_len)
{
hits_list[i].dseq = (char*) xmalloc(seq_len);
memcpy(hits_list[i].dseq, seq, seq_len);
hits_list[i].dlen = seq_len;
}
void hits_enter_align_hint(long i, long q_end, long d_end)
{
hits_list[i].bestq = q_end;
hits_list[i].align_hint = d_end;
}
void hits_enter_align_coord(long i,
long align_q_start,
long align_q_end,
long align_d_start,
long align_d_end,
long dlennt)
{
hits_list[i].align_q_start = align_q_start;
hits_list[i].align_q_end = align_q_end;
hits_list[i].align_d_start = align_d_start;
hits_list[i].align_d_end = align_d_end;
hits_list[i].dlennt = dlennt;
}
void hits_enter_header(long i, char * header, long header_len)
{
hits_list[i].header_address = (char*) xmalloc(header_len);
memcpy(hits_list[i].header_address, header, header_len);
hits_list[i].header_length = header_len;
}
void hits_enter_align_string(long i, char * align, long align_len)
{
hits_list[i].alignment = (char*) xmalloc(align_len);
memcpy(hits_list[i].alignment, align, align_len);
// hits_list[i].alignment[align_len] = 0;
}
void hits_init(long descriptions, long alignments, long minscore, long maxscore, double minexpect, double expect, int show_nostats)
{
opt_descriptions = descriptions;
opt_alignments = alignments;
keephits = descriptions > alignments ? descriptions : alignments;
long maxhits = db_getseqcount_masked();
if (symtype == 0)
{
if (querystrands == 3)
maxhits *= 2;
}
else if (symtype == 2)
{
if (querystrands == 3)
maxhits *= 6;
else
maxhits *= 3;
}
else if (symtype == 3)
{
maxhits *= 6;
}
else if (symtype == 4)
{
if (querystrands == 3)
maxhits *= 36;
else
maxhits *= 18;
}
if (keephits > maxhits)
keephits = maxhits;
obvious = 0;
hits_count = 0;
hits_list = (struct hits_entry *) xmalloc(keephits * sizeof(struct hits_entry));
for(int i=0; i<keephits; i++)
{
struct hits_entry * h = hits_list + i;
h->header_address = 0;
h->header_length = 0;
h->dseq = 0;
h->alignment = 0;
}
int seqcount;
long symcount;
if (db_ismasked())
{
seqcount = db_getseqcount_masked();
symcount = db_getsymcount_masked();
}
else
{
seqcount = db_getseqcount();
symcount = db_getsymcount();
}
//fprintf(out, "matrix=%s, go=%ld, ge=%ld\n", matrixname, gapopen, gapextend);
stats_available = 0;
long m = 0;
long n = 0;
int lenadj = 0;
if (symtype == 0)
{
if (stats_getparams_nt(matchscore,
mismatchscore,
gapopen,
gapextend,
& lambda,
& K,
& H,
& alpha,
& beta))
{
stats_available = 1;
/*
fprintf(out, "Params: lambda=%6.3g K=%6.3g H=%6.3g alpha=%6.3g beta=%6.3g\n",
lambda, K, H, alpha, beta);
*/
logK = log(K);
lambda_d_log2 = lambda / log(2.0);
logK_d_log2 = logK / log(2.0);
lenadj = 0;
long qlen = query.nt[0].len;
long dlen;
if (effdbsize > 0)
dlen = effdbsize;
else
dlen = symcount;
BlastComputeLengthAdjustment(K,
logK,
alpha / lambda,
beta,
qlen,
dlen,
seqcount,
& lenadj);
// fprintf(out, "lenadj: %d\n", lenadj);
m = qlen - lenadj;
if (effdbsize > 0)
n = effdbsize;
else
n = dlen - seqcount * lenadj;
Kmn = K * (double)m * (double)n;
}
}
else if (symtype < 5)
{
if (symtype == 4)
{
stats_available = stats_getparams(matrixname,
32767,
32767,
& lambda,
& K,
& H,
& alpha,
& beta);
}
else
{
stats_available = stats_getparams(matrixname,
gapopen,
gapextend,
& lambda,
& K,
& H,
& alpha,
& beta);
}
if (stats_available)
{
#ifdef DEBUG
fprintf(out, "Params: lambda=%6.3g K=%6.3g H=%6.3g alpha=%6.3g beta=%6.3g\n",
lambda, K, H, alpha, beta);
#endif
logK = log(K);
lambda_d_log2 = lambda / log(2.0);
logK_d_log2 = logK / log(2.0);
lenadj = 0;
long qlen = query.aa[0].len;
if ((symtype == 2) || (symtype == 4))
qlen = query.nt[0].len / 3;
long dlen;
if (effdbsize > 0)
{
dlen = effdbsize;
}
else
{
if ((symtype == 3) || (symtype == 4))
dlen = symcount / 3;
else
dlen = symcount;
}
BlastComputeLengthAdjustment(K,
logK,
alpha / lambda,
beta,
qlen,
dlen,
seqcount,
& lenadj);
m = qlen - lenadj;
if (effdbsize > 0)
n = effdbsize;
else
n = dlen - seqcount * lenadj;
Kmn = K * (double)m * (double)n;
}
}
#ifdef DEBUG
fprintf(out, "lenadj=%d m=%ld n=%ld mn=%.1f\n", lenadj, m, n, (double)m * (double)n);
#endif
scorethreshold = minscore;
upperscorethreshold = maxscore;
if (stats_available)
{
long minscore_expect = (long)(ceil(- log(expect / Kmn) / lambda));
if (minscore_expect > minscore)
scorethreshold = minscore_expect;
if (minexpect > 0.0)
{
long maxscore_expect = (long)(floor(- log(minexpect / Kmn) / lambda));
if (maxscore_expect < maxscore)
upperscorethreshold = maxscore_expect;
}
}
else
{
if (show_nostats)
fprintf(out, "Statistical parameters are not available for the scoring system specified.\nBit scores and E-values will not be computed.\n\n");
}
init_threshold = scorethreshold;
// fprintf(out, "scorethreshold: %ld\n", scorethreshold);
}
void hits_empty()
{
for (long i=0; i<hits_count; i++)
{
struct hits_entry * h = hits_list + i;
if (h->header_address)
{
free(h->header_address);
h->header_address = 0;
}
if (h->dseq)
{
free(h->dseq);
h->dseq = 0;
}
if (h->alignment)
{
free(h->alignment);
h->alignment = 0;
}
}
}
void hits_exit()
{
hits_empty();
free(hits_list);
hits_list = 0;
}
void hits_align(struct db_thread_s * t, long i)
{
char * address;
long length, ntlen;
struct hits_entry * h = hits_list + i;
db_mapheaders(t, h->seqno, h->seqno);
db_getheader(t, h->seqno, & address, & length);
h->header_length = length;
h->header_address = (char*) xmalloc(length);
memcpy(h->header_address, address, length);
if (i < opt_alignments)
{
db_mapsequences(t, h->seqno, h->seqno);
db_getsequence(t, h->seqno, h->dstrand, h->dframe,
& address, & length, & ntlen, 0);
h->dlen = length - 1;
h->dlennt = ntlen;
h->dseq = (char*)xmalloc(h->dlen);
memcpy(h->dseq, address, h->dlen);
char * qseq;
long qlen;
if (symtype == 0)
{
qseq = query.nt[0].seq;
qlen = query.nt[0].len;
}
else
{
qseq = query.aa[3*h->qstrand + h->qframe].seq;
qlen = query.aa[3*h->qstrand + h->qframe].len;
}
// give hint of alignment end
if ((h->bestq > 0) && (h->align_hint))
{
h->score_align = h->score;
h->align_q_end = h->bestq;
h->align_d_end = h->align_hint;
#if 0
printf("Align with hints: score=%ld, q_end=%ld, d_end=%ld\n",
h->score_align, h->align_q_end, h->align_d_end);
#endif
}
else
{
h->score_align = 0;
h->align_q_end = 0;
h->align_d_end = 0;
}
align(qseq,
h->dseq,
qlen,
h->dlen,
score_matrix_63,
gapopen,
gapextend,
& h->align_q_start,
& h->align_d_start,
& h->align_q_end,
& h->align_d_end,
& h->alignment,
& h->score_align);
}
}
#define ALIGNLEN 60
long line_pos;
long q_start;
long d_start;
long q_pos;
long d_pos;
long q_len;
long q_len_nt;
long d_len;
long d_len_nt;
long d_strand;
long d_frame;
long q_strand;
long q_frame;
long q_first;
long q_last;
long d_first;
long d_last;
char * q_seq;
char * d_seq;
char q_line[ALIGNLEN+1];
char a_line[ALIGNLEN+1];
char d_line[ALIGNLEN+1];
const char * sym;
int poswidth;
void putalignop(char c, long len)
{
long count = len;
while(count)
{
if (line_pos == 0)
{
q_start = q_pos;
d_start = d_pos;
}
char qs;
char ds;
switch(c)
{
case 'M':
qs = q_seq[q_pos++];
ds = d_seq[d_pos++];
q_line[line_pos] = sym[(int)(qs)];
if (symtype == 0)
{
a_line[line_pos] = (qs == ds) ? '|' : ' ';
}
else
{
a_line[line_pos] = (qs == ds) ? sym[(int)(qs)] :
(score_matrix_63[32*qs+ds] > 0 ? '+' : ' ');
}
d_line[line_pos] = sym[(int)(ds)];
line_pos++;
break;
case 'D':
qs = q_seq[q_pos++];
q_line[line_pos] = sym[(int)(qs)];
a_line[line_pos] = ' ';
d_line[line_pos] = '-';
line_pos++;
break;
case 'I':
ds = d_seq[d_pos++];
q_line[line_pos] = '-';
a_line[line_pos] = ' ';
d_line[line_pos] = sym[(int)(ds)];
line_pos++;
break;
}
if ((line_pos == ALIGNLEN) || ((c == 0) && (line_pos > 0)))
{
// print alignment lines
q_line[line_pos] = 0;
a_line[line_pos] = 0;
d_line[line_pos] = 0;
long q1 = q_start + 1;
long q2 = q_pos;
long d1 = d_start + 1;
long d2 = d_pos;
if (symtype == 0)
{
if (d_strand)
{
d1 = d_len - d1 + 1;
d2 = d_len - d2 + 1;
}
}
if ((symtype == 2) || (symtype == 4))
{
if (q_strand)
{
q1 = q_len_nt - 3*q_start - q_frame;
q2 = q_len_nt - 3*q_pos - q_frame + 1;
}
else
{
q1 = 3*q_start + q_frame + 1;
q2 = 3*q_pos + q_frame;
}
}
if ((symtype == 3) || (symtype == 4))
{
if (d_strand)
{
d1 = d_len_nt - 3*d_start - d_frame;
d2 = d_len_nt - 3*d_pos - d_frame + 1;
}
else
{
d1 = 3*d_start + d_frame + 1;
d2 = 3*d_pos + d_frame;
}
}
fprintf(out, "\n");
fprintf(out, "Query: %*ld %s %ld\n", poswidth, q1, q_line, q2);
fprintf(out, " %*s %s\n", poswidth, "", a_line);
fprintf(out, "Sbjct: %*ld %s %ld\n", poswidth, d1, d_line, d2);
line_pos = 0;
}
count--;
}
}
void show_align(long i)
{
long q_align_start = hits_list[i].align_q_start;
long d_align_start = hits_list[i].align_d_start;
q_strand = hits_list[i].qstrand;
q_frame = hits_list[i].qframe;
d_strand = hits_list[i].dstrand;
d_frame = hits_list[i].dframe;
char * alignment = hits_list[i].alignment;
if (symtype == 0)
{
sym = sym_ncbi_nt16;
q_seq = query.nt[0].seq;
q_len = query.nt[0].len;
}
else if (symtype == 5)
{
sym = sym_sound;
q_seq = query.aa[0].seq;
q_len = query.aa[0].len;
}
else
{
sym = sym_ncbi_aa;
q_seq = query.aa[3*q_strand+q_frame].seq;
q_len = query.aa[3*q_strand+q_frame].len;
q_len_nt = query.nt[0].len;
d_len_nt = hits_list[i].dlennt;
}
d_seq = hits_list[i].dseq;
d_len = hits_list[i].dlen;
q_pos = q_align_start;
d_pos = d_align_start;
char * p = alignment;
char * e = alignment + strlen(alignment);
while(p < e)
{
char op = *p++;
long len;
int n;
sscanf(p, "%ld%n", & len, & n);
p += n;
putalignop(op, len);
}
putalignop(0, 1);
}
void whole_align(long i,
long * identities,
long * positives,
long * indels,
long * aligned,
long * gaps,
char ** qline,
char ** aline,
char ** dline)
{
long al = 0;
char * alignment = hits_list[i].alignment;
char * p = alignment;
while(*p)
{
long len;
int n;
sscanf(p, "%*c%ld%n", & len, & n);
p += n;
al += len;
}
char * qlinep = (char*) xmalloc(al+1);
char * alinep = (char*) xmalloc(al+1);
char * dlinep = (char*) xmalloc(al+1);
*qline = qlinep;
*aline = alinep;
*dline = dlinep;
long q_align_start = hits_list[i].align_q_start;
long d_align_start = hits_list[i].align_d_start;
d_strand = hits_list[i].dstrand;
d_frame = hits_list[i].dframe;
q_strand = hits_list[i].qstrand;
q_frame = hits_list[i].qframe;
if (symtype == 0)
{
sym = sym_ncbi_nt16;
q_seq = query.nt[q_strand].seq;
q_len = query.nt[q_strand].len;
}
else if (symtype == 5)
{
sym = sym_sound;
q_seq = query.aa[0].seq;
q_len = query.aa[0].len;
}
else
{
sym = sym_ncbi_aa;
q_seq = query.aa[3*q_strand+q_frame].seq;
q_len = query.aa[3*q_strand+q_frame].len;
q_len_nt = query.nt[0].len;
d_len_nt = hits_list[i].dlennt;
}
*identities = 0;
*positives = 0;
*indels = 0;
*gaps = 0;
*aligned = 0;
d_seq = hits_list[i].dseq;
d_len = hits_list[i].dlen;
q_pos = q_align_start;
d_pos = d_align_start;
p = alignment;
while(*p)
{
char op = *p++;
long len;
int n;
sscanf(p, "%ld%n", & len, & n);
p += n;
*aligned += len;
if (op == 'D')
{
for(long j=0; j<len; j++)
{
char qs = q_seq[q_pos++];
*qlinep++ = sym[(int)(qs)];
*alinep++ = ' ';
*dlinep++ = '-';
}
*gaps += 1;
*indels += len;
}
else if (op == 'I')
{
for(long j=0; j<len; j++)
{
char ds = d_seq[d_pos++];
*qlinep++ = '-';
*alinep++ = ' ';
*dlinep++ = sym[(int)(ds)];
}
*gaps += 1;
*indels += len;
}
else if (op == 'M')
{
for(long j=0; j<len; j++)
{
char qs = q_seq[q_pos++];
char ds = d_seq[d_pos++];
*qlinep++ = sym[(int)(qs)];
if (qs == ds)
{
*alinep++ = '|';
(*identities)++;
(*positives)++;
}
else if (score_matrix_63[32*qs+ds] > 0)
{
*alinep++ = '+';
(*positives)++;
}
else
{
*alinep++ = ' ';
}
*dlinep++ = sym[(int)(ds)];
}
}
else
fatal("Illegal alignment string.");
}
*qlinep = 0;
*alinep = 0;
*dlinep = 0;
/* calculate first and last alignment positions for display */
q_first = hits_list[i].align_q_start;
q_last = hits_list[i].align_q_end;
d_first = hits_list[i].align_d_start;
d_last = hits_list[i].align_d_end;
if (symtype == 0)
{
if (q_strand)
{
q_first = q_len - 1 - q_first;
q_last = q_len - 1 - q_last;
}
if (d_strand)
{
d_first = d_len - 1 - d_first;
d_last = d_len - 1 - d_last;
}
}
if ((symtype == 2) || (symtype == 4))
{
if (q_strand)
{
q_first = query.nt[0].len - 1 - 3 * q_first - q_frame;
q_last = query.nt[0].len - 1 - 3 * q_last - q_frame - 2;
}
else
{
q_first = 3 * q_first + q_frame;
q_last = 3 * q_last + q_frame + 2;
}
}
if ((symtype == 3) || (symtype == 4))
{
if (d_strand)
{
d_first = d_len_nt - 1 - 3 * d_first - d_frame;
d_last = d_len_nt - 1 - 3 * d_last - d_frame - 2;
}
else
{
d_first = 3 * d_first + d_frame;