/
cdhit-common.c++
4408 lines (4076 loc) · 142 KB
/
cdhit-common.c++
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// =============================================================================
// CD-HI/CD-HIT
//
// Cluster Database at High Identity
//
// CD-HIT clusters protein sequences at high identity threshold.
// This program can remove the high sequence redundance efficiently.
//
// program written by
// Weizhong Li
// UCSD, San Diego Supercomputer Center
// La Jolla, CA, 92093
// Email liwz@sdsc.edu
//
// at
// Adam Godzik's lab
// The Burnham Institute
// La Jolla, CA, 92037
// Email adam@burnham-inst.org
//
// modified by:
// Limin Fu
// Center for Research in Biological Systems (CRBS), UCSD
// La Jolla, CA, 92093
// Email: l2fu@ucsd.edu, fu@daovm.net
// =============================================================================
#include "cdhit-common.h"
#include<valarray>
#include<stdint.h>
#include<assert.h>
#include<limits.h>
#ifndef NO_OPENMP
#include<omp.h>
#define WITH_OPENMP " (+OpenMP)"
#else
#define WITH_OPENMP ""
#define omp_set_num_threads(T) (T = T)
#define omp_get_thread_num() 0
#endif
//class function definition
const char aa[] = {"ARNDCQEGHILKMFPSTWYVBZX"};
//{0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,2,6,20};
int aa2idx[] = {0, 2, 4, 3, 6, 13,7, 8, 9,20,11,10,12, 2,20,14,
5, 1,15,16,20,19,17,20,18, 6};
// idx for A B C D E F G H I J K L M N O P
// Q R S T U V W X Y Z
// so aa2idx[ X - 'A'] => idx_of_X, eg aa2idx['A' - 'A'] => 0,
// and aa2idx['M'-'A'] => 12
int BLOSUM62[] = {
4, // A
-1, 5, // R
-2, 0, 6, // N
-2,-2, 1, 6, // D
0,-3,-3,-3, 9, // C
-1, 1, 0, 0,-3, 5, // Q
-1, 0, 0, 2,-4, 2, 5, // E
0,-2, 0,-1,-3,-2,-2, 6, // G
-2, 0, 1,-1,-3, 0, 0,-2, 8, // H
-1,-3,-3,-3,-1,-3,-3,-4,-3, 4, // I
-1,-2,-3,-4,-1,-2,-3,-4,-3, 2, 4, // L
-1, 2, 0,-1,-3, 1, 1,-2,-1,-3,-2, 5, // K
-1,-1,-2,-3,-1, 0,-2,-3,-2, 1, 2,-1, 5, // M
-2,-3,-3,-3,-2,-3,-3,-3,-1, 0, 0,-3, 0, 6, // F
-1,-2,-2,-1,-3,-1,-1,-2,-2,-3,-3,-1,-2,-4, 7, // P
1,-1, 1, 0,-1, 0, 0, 0,-1,-2,-2, 0,-1,-2,-1, 4, // S
0,-1, 0,-1,-1,-1,-1,-2,-2,-1,-1,-1,-1,-2,-1, 1, 5, // T
-3,-3,-4,-4,-2,-2,-3,-2,-2,-3,-2,-3,-1, 1,-4,-3,-2,11, // W
-2,-2,-2,-3,-2,-1,-2,-3, 2,-1,-1,-2,-1, 3,-3,-2,-2, 2, 7, // Y
0,-3,-3,-3,-1,-2,-2,-3,-3, 3, 1,-2, 1,-1,-2,-2, 0,-3,-1, 4, // V
-2,-1, 3, 4,-3, 0, 1,-1, 0,-3,-4, 0,-3,-3,-2, 0,-1,-4,-3,-3, 4, // B
-1, 0, 0, 1,-3, 3, 4,-2, 0,-3,-3, 1,-1,-3,-1, 0,-1,-3,-2,-2, 1, 4, // Z
0,-1,-1,-1,-2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-2, 0, 0,-2,-1,-1,-1,-1,-1 // X
//A R N D C Q E G H I L K M F P S T W Y V B Z X
//0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 2 6 20
};
int na2idx[] = {0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 3, 3, 4, 4, 4, 4, 4};
// idx for A B C D E F G H I J K L M N O P
// Q R S T U V W X Y Z
// so aa2idx[ X - 'A'] => idx_of_X, eg aa2idx['A' - 'A'] => 0,
// and aa2idx['M'-'A'] => 4
int BLOSUM62_na[] = {
2, // A
-2, 2, // C
-2,-2, 2, // G
-2,-2,-2, 2, // T
-2,-2,-2, 1, 2, // U
-2,-2,-2,-2,-2, 1, // N
0, 0, 0, 0, 0, 0, 1 // X
//A C G T U N X
//0 1 2 3 3 4 5
};
void setaa_to_na();
struct TempFile
{
FILE *file;
char buf[512];
TempFile( const char *dir = NULL ){
int len = dir ? strlen( dir ) : 0;
assert( len < 400 );
buf[0] = 0;
if( len ){
strcat( buf, dir );
if( buf[len-1] != '/' && buf[len-1] != '\\' ){
buf[len] = '/';
len += 1;
}
}
strcat( buf, "cdhit.temp." );
len += 11;
sprintf( buf + len, "%p", this );
file = fopen( buf, "w+" );
}
~TempFile(){
if( file ){
fclose( file );
remove( buf );
}
}
};
struct TempFiles
{
NVector<TempFile*> files;
~TempFiles(){ Clear(); }
void Clear(){
int i;
#pragma omp critical
{
for(i=0; i<files.size; i++) if( files[i] ) delete files[i];
files.Clear();
}
}
};
const char *temp_dir = "";
TempFiles temp_files;
FILE* OpenTempFile( const char *dir = NULL )
{
TempFile *file = new TempFile( dir );
#pragma omp critical
{
temp_files.files.Append( file );
}
return file->file;
}
static void CleanUpTempFiles()
{
if( temp_files.files.Size() ) printf( "Clean up temporary files ...\n" );
temp_files.Clear();
}
int NAA1 ;
int NAA2 ;
int NAA3 ;
int NAA4 ;
int NAA5 ;
int NAA6 ;
int NAA7 ;
int NAA8 ;
int NAA9 ;
int NAA10;
int NAA11;
int NAA12;
int NAAN_array[13] = { 1 };
void InitNAA( int max )
{
NAA1 = NAAN_array[1] = max;
NAA2 = NAAN_array[2] = NAA1 * NAA1;
NAA3 = NAAN_array[3] = NAA1 * NAA2;
NAA4 = NAAN_array[4] = NAA2 * NAA2;
NAA5 = NAAN_array[5] = NAA2 * NAA3;
NAA6 = NAAN_array[6] = NAA3 * NAA3;
NAA7 = NAAN_array[7] = NAA3 * NAA4;
NAA8 = NAAN_array[8] = NAA4 * NAA4;
NAA9 = NAAN_array[9] = NAA4 * NAA5;
NAA10 = NAAN_array[10] = NAA5 * NAA5;
NAA11 = NAAN_array[11] = NAA5 * NAA6;
NAA12 = NAAN_array[12] = NAA6 * NAA6;
}
extern Options options;
ScoreMatrix mat;
Vector<int> Comp_AAN_idx;
void make_comp_iseq(int len, char *iseq_comp, char *iseq)
{
int i, c[6] = {3,2,1,0,4,5};
for (i=0; i<len; i++) iseq_comp[i] = c[ (int)iseq[len-i-1] ];
} // make_comp_iseq
bool Options::SetOptionCommon( const char *flag, const char *value )
{
int intval = atoi( value );
if (strcmp(flag, "-i" ) == 0) input = value;
else if (strcmp(flag, "-j" ) == 0) input_pe = value;
else if (strcmp(flag, "-o" ) == 0) output = value;
else if (strcmp(flag, "-op") == 0) output_pe = value;
else if (strcmp(flag, "-M" ) == 0) max_memory = atoll(value) * 1000000;
else if (strcmp(flag, "-l" ) == 0) min_length = intval;
else if (strcmp(flag, "-c" ) == 0) cluster_thd = atof(value), useIdentity = true;
else if (strcmp(flag, "-D" ) == 0) distance_thd = atof(value), useDistance = true;
else if (strcmp(flag, "-b" ) == 0) band_width = intval;
else if (strcmp(flag, "-n" ) == 0) NAA = intval;
else if (strcmp(flag, "-d" ) == 0) des_len = intval;
else if (strcmp(flag, "-s" ) == 0) diff_cutoff = atof(value);
else if (strcmp(flag, "-S" ) == 0) diff_cutoff_aa = intval;
else if (strcmp(flag, "-B" ) == 0) store_disk = intval;
else if (strcmp(flag, "-P" ) == 0) PE_mode = intval;
else if (strcmp(flag, "-cx") == 0) trim_len = intval;
else if (strcmp(flag, "-cy") == 0) trim_len_R2 = intval;
else if (strcmp(flag, "-ap") == 0) align_pos = intval;
else if (strcmp(flag, "-sc") == 0) sort_output = intval;
else if (strcmp(flag, "-sf") == 0) sort_outputf = intval;
else if (strcmp(flag, "-p" ) == 0) print = intval;
else if (strcmp(flag, "-g" ) == 0) cluster_best = intval;
else if (strcmp(flag, "-G" ) == 0) global_identity = intval;
else if (strcmp(flag, "-aL") == 0) long_coverage = atof(value);
else if (strcmp(flag, "-AL") == 0) long_control = intval;
else if (strcmp(flag, "-aS") == 0) short_coverage = atof(value);
else if (strcmp(flag, "-AS") == 0) short_control = intval;
else if (strcmp(flag, "-A" ) == 0) min_control = intval;
else if (strcmp(flag, "-uL") == 0) long_unmatch_per = atof(value);
else if (strcmp(flag, "-uS") == 0) short_unmatch_per = atof(value);
else if (strcmp(flag, "-U") == 0) unmatch_len = intval;
else if (strcmp(flag, "-tmp" ) == 0) temp_dir = value;
else if (strcmp(flag, "-bak" ) == 0) backupFile = intval;
else if (strcmp(flag, "-T" ) == 0){
#ifndef NO_OPENMP
int cpu = omp_get_num_procs();
threads = intval;
if( threads > cpu ){
threads = cpu;
printf( "Warning: total number of CPUs in the system is %i\n", cpu );
}else if( threads < 0 ){
threads += cpu;
if( threads < 0 ) threads = 0;
}
if( threads == 0 ){
threads = cpu;
printf( "total number of CPUs in the system is %i\n", cpu );
}
if( threads != intval ) printf( "Actual number of CPUs to be used: %i\n\n", threads );
#else
printf( "Option -T is ignored: multi-threading with OpenMP is NOT enabled!\n" );
#endif
}else return false;
return true;
}
bool Options::SetOption( const char *flag, const char *value )
{
if( is454 ){
if( strcmp(flag, "-s") == 0 ) return false;
else if( strcmp(flag, "-S") == 0 ) return false;
else if( strcmp(flag, "-G") == 0 ) return false;
else if( strcmp(flag, "-A") == 0 ) return false;
else if( strcmp(flag, "-r") == 0 ) return false;
else if( strcmp(flag, "-D") == 0 ){ max_indel = atoi(value); return true; }
}
if( SetOptionCommon( flag, value ) ) return true;
if (strcmp(flag, "-t" ) == 0) tolerance = atoi(value);
else if (strcmp(flag, "-F" ) == 0) frag_size = atoi(value);
else if (has2D && SetOption2D( flag, value ) ) return true;
else if (isEST && SetOptionEST( flag, value ) ) return true;
else return false;
return true;
}
bool Options::SetOption2D( const char *flag, const char *value )
{
if( SetOptionCommon( flag, value ) ) return true;
if (strcmp(flag, "-i2" ) == 0) input2 = value;
else if (strcmp(flag, "-j2" ) == 0) input2_pe = value;
else if (strcmp(flag, "-s2") == 0) diff_cutoff2 = atof(value);
else if (strcmp(flag, "-S2") == 0) diff_cutoff_aa2 = atoi(value);
else return false;
return true;
}
bool Options::SetOptionEST( const char *flag, const char *value )
{
NAA_top_limit = 12;
if( SetOptionCommon( flag, value ) ) return true;
if (strcmp(flag, "-r" ) == 0) option_r = atoi(value);
else if (strcmp(flag, "-gap") == 0) mat.gap = MAX_SEQ * atoi(value);
else if (strcmp(flag, "-gap-ext") == 0) mat.ext_gap = MAX_SEQ * atoi(value);
else if (strcmp(flag, "-match") == 0) mat.set_match( atoi(value) );
else if (strcmp(flag, "-mismatch") == 0) mat.set_mismatch( atoi(value) );
else if (strcmp(flag, "-mask") == 0){
string letters = value;
int i, n = letters.size();
for(i=0; i<n; i++){
char ch = toupper( letters[i] );
if( ch < 'A' || ch > 'Z' ) continue;
na2idx[ ch - 'A' ] = 5;
}
setaa_to_na();
}else return false;
return true;
}
bool Options::SetOptions( int argc, char *argv[], bool twod, bool est )
{
int i, n;
char date[100];
strcpy( date, __DATE__ );
n = strlen( date );
for(i=1; i<n; i++) if( date[i-1] == ' ' and date[i] == ' ' ) date[i] = '0';
printf( "================================================================\n" );
printf( "Program: CD-HIT, V" CDHIT_VERSION WITH_OPENMP ", %s, " __TIME__ "\n", date );
printf( "Command:" );
n = 9;
for(i=0; i<argc; i++){
n += strlen( argv[i] ) + 1;
if( n >= 64 ){
printf( "\n %s", argv[i] );
n = strlen( argv[i] ) + 9;
}else{
printf( " %s", argv[i] );
}
}
printf( "\n\n" );
time_t tm = time(NULL);
printf( "Started: %s", ctime(&tm) );
printf( "================================================================\n" );
printf( " Output \n" );
printf( "----------------------------------------------------------------\n" );
has2D = twod;
isEST = est;
for (i=1; i+1<argc; i+=2) if ( SetOption( argv[i], argv[i+1] ) == 0) return false;
if( i < argc ) return false;
atexit( CleanUpTempFiles );
return true;
}
void Options::Validate()
{
if( useIdentity and useDistance ) bomb_error( "can not use both identity cutoff and distance cutoff" );
if( useDistance ){
if ((distance_thd > 1.0) || (distance_thd < 0.0)) bomb_error("invalid distance threshold");
}else if( isEST ){
if ((cluster_thd > 1.0) || (cluster_thd < 0.8)) bomb_error("invalid clstr threshold, should >=0.8");
}else{
if ((cluster_thd > 1.0) || (cluster_thd < 0.4)) bomb_error("invalid clstr");
}
if (input.size() == 0) bomb_error("no input file");
if (output.size() == 0) bomb_error("no output file");
if (PE_mode) {
if (input_pe.size() == 0) bomb_error("no input file for R2 sequences in PE mode");
if (output_pe.size() == 0) bomb_error("no output file for R2 sequences in PE mode");
}
if (isEST && (align_pos==1)) option_r = 0;
if (band_width < 1 ) bomb_error("invalid band width");
if (NAA < 2 || NAA > NAA_top_limit) bomb_error("invalid word length");
if (des_len < 0 ) bomb_error("too short description, not enough to identify sequences");
if (not isEST && (tolerance < 0 || tolerance > 5) ) bomb_error("invalid tolerance");
if ((diff_cutoff<0) || (diff_cutoff>1)) bomb_error("invalid value for -s");
if (diff_cutoff_aa<0) bomb_error("invalid value for -S");
if( has2D ){
if ((diff_cutoff2<0) || (diff_cutoff2>1)) bomb_error("invalid value for -s2");
if (diff_cutoff_aa2<0) bomb_error("invalid value for -S2");
if (PE_mode) {
if (input2_pe.size() == 0) bomb_error("no input file for R2 sequences for 2nd db in PE mode");
}
}
if (global_identity == 0) print = 1;
if (short_coverage < long_coverage) short_coverage = long_coverage;
if (short_control > long_control) short_control = long_control;
if ((global_identity == 0) && (short_coverage == 0.0) && (min_control == 0))
bomb_error("You are using local identity, but no -aS -aL -A option");
if (frag_size < 0) bomb_error("invalid fragment size");
#if 0
if( useDistance ){
/* when required_aan becomes zero */
if( distance_thd * NAA >= 1 )
bomb_warning( "word length is too long for the distance cutoff" );
}else{
/* when required_aan becomes zero */
if( cluster_thd <= 1.0 - 1.0 / NAA )
bomb_warning( "word length is too long for the identity cutoff" );
}
#endif
const char *message = "Your word length is %i, using %i may be faster!\n";
if ( not isEST && tolerance ) {
int i, clstr_idx = (int) (cluster_thd * 100) - naa_stat_start_percent;
int tcutoff = naa_stat[tolerance-1][clstr_idx][5-NAA];
if (tcutoff < 5 )
bomb_error("Too low cluster threshold for the word length.\n"
"Increase the threshold or the tolerance, or decrease the word length.");
for ( i=5; i>NAA; i--) {
if ( naa_stat[tolerance-1][clstr_idx][5-i] > 10 ) {
printf( message, NAA, i );
break;
}
}
} else if( isEST ) {
if ( cluster_thd > 0.9 && NAA < 8 ) printf( message, NAA, 8 );
else if ( cluster_thd > 0.87 && NAA < 5 ) printf( message, NAA, 5 );
else if ( cluster_thd > 0.80 && NAA < 4 ) printf( message, NAA, 4 );
else if ( cluster_thd > 0.75 && NAA < 3 ) printf( message, NAA, 3 );
} else {
if ( cluster_thd > 0.85 && NAA < 5 ) printf( message, NAA, 5 );
else if ( cluster_thd > 0.80 && NAA < 4 ) printf( message, NAA, 4 );
else if ( cluster_thd > 0.75 && NAA < 3 ) printf( message, NAA, 3 );
}
if ( (min_length + 1) < NAA ) bomb_error("Too short -l, redefine it");
}
void Options::Print()
{
printf( "isEST = %i\n", isEST );
printf( "has2D = %i\n", has2D );
printf( "NAA = %i\n", NAA );
printf( "NAA_top_limit = %i\n", NAA_top_limit );
printf( "min_length = %i\n", min_length );
printf( "cluster_best = %i\n", cluster_best );
printf( "global_identity = %i\n", global_identity );
printf( "cluster_thd = %g\n", cluster_thd );
printf( "diff_cutoff = %g\n", diff_cutoff );
printf( "diff_cutoff_aa = %i\n", diff_cutoff_aa );
printf( "tolerance = %i\n", tolerance );
printf( "long_coverage = %g\n", long_coverage );
printf( "long_control = %i\n", long_control );
printf( "short_coverage = %g\n", short_coverage );
printf( "short_control = %i\n", short_control );
printf( "frag_size = %i\n", frag_size );
printf( "option_r = %i\n", option_r );
printf( "print = %i\n", print );
}
void bomb_error(const char *message)
{
fprintf( stderr, "\nFatal Error:\n%s\nProgram halted !!\n\n", message );
temp_files.Clear();
exit (1);
} // END void bomb_error
void bomb_error(const char *message, const char *message2)
{
fprintf( stderr, "\nFatal Error:\n%s %s\nProgram halted !!\n\n", message, message2 );
temp_files.Clear();
exit (1);
} // END void bomb_error
void bomb_warning(const char *message)
{
fprintf( stderr, "\nWarning:\n%s\nNot fatal, but may affect results !!\n\n", message );
} // END void bomb_warning
void bomb_warning(const char *message, const char *message2)
{
fprintf( stderr, "\nWarning:\n%s %s\nNot fatal, but may affect results !!\n\n", message, message2 );
} // END void bomb_warning
void format_seq(char *seq)
{
int i, j;
char c1;
int len = strlen(seq);
for (i=0,j=0; i<len; i++) {
c1 = toupper(seq[i]);
if ( isalpha(c1) ) seq[j++] = c1;
}
seq[j] = 0;
} // END void format_seq
void strrev(char *p)
{
char *q = p;
while(q && *q) ++q;
for(--q; p < q; ++p, --q)
*p = *p ^ *q,
*q = *p ^ *q,
*p = *p ^ *q;
}
////For smiple len1 <= len2, len2 is for existing representative
////walk along all diag path of two sequences,
////find the diags with most aap
////return top n diags
////added on 2006 11 13
////band 0 XXXXXXXXXXXXXXXXXX seq2, rep seq
//// XXXXXXXXXXXXXXX seq1
////band 1 XXXXXXXXXXXXXXXXXX seq2, rep seq
//// XXXXXXXXXXXXXXX seq1
////extreme right (+) XXXXXXXXXXXXXXXXXX seq2, rep seq
//// band = len2-1 XXXXXXXXXXXXXXX seq1
////band-1 XXXXXXXXXXXXXXXXXX seq2, rep seq
//// XXXXXXXXXXXXXXX seq1
////extreme left (-) XXXXXXXXXXXXXXXXXX seq2, rep seq
//// XXXXXXXXXXXXXXX band = -(len1-1) seq1
////index of diag_score = band+len1-1;
int diag_test_aapn(int NAA1, char iseq2[], int len1, int len2, WorkingBuffer & buffer,
int &best_sum, int band_width, int &band_left, int &band_center, int &band_right, int required_aa1)
{
int i, i1, j, k;
int *pp;
int nall = len1+len2-1;
Vector<int> & taap = buffer.taap;
Vector<INTs> & aap_begin = buffer.aap_begin;
Vector<INTs> & aap_list = buffer.aap_list;
Vector<int> & diag_score = buffer.diag_score;
Vector<int> & diag_score2 = buffer.diag_score2;
if (nall > MAX_DIAG) bomb_error("in diag_test_aapn, MAX_DIAG reached");
for (pp=&diag_score[0], i=nall; i; i--, pp++) *pp=0;
for (pp=&diag_score2[0], i=nall; i; i--, pp++) *pp=0;
int c22, cpx;
INTs *bip;
int len11 = len1-1;
int len22 = len2-1;
i1 = len11;
for (i=0; i<len22; i++,i1++) {
c22 = iseq2[i]*NAA1+ iseq2[i+1];
cpx = 1 + (iseq2[i] != iseq2[i+1]);
if ( (j=taap[c22]) == 0) continue;
int m = aap_begin[c22];
for(int k=0; k<j; k++){
diag_score[ i1 - aap_list[m+k] ] ++;
diag_score2[ i1 - aap_list[m+k] ] += cpx;
}
}
//find the best band range
// int band_b = required_aa1;
int band_b = required_aa1-1 >= 0 ? required_aa1-1:0; // on dec 21 2001
int band_e = nall - band_b;
int band_m = ( band_b+band_width-1 < band_e ) ? band_b+band_width-1 : band_e;
int best_score=0;
int best_score2=0;
int max_diag = 0;
int max_diag2 = 0;
int imax_diag = 0;
for (i=band_b; i<=band_m; i++){
best_score += diag_score[i];
best_score2 += diag_score2[i];
if( diag_score2[i] > max_diag2 ){
max_diag2 = diag_score2[i];
max_diag = diag_score[i];
imax_diag = i;
}
}
int from=band_b;
int end =band_m;
int score = best_score;
int score2 = best_score2;
for (k=from, j=band_m+1; j<band_e; j++, k++) {
score -= diag_score[k];
score += diag_score[j];
score2 -= diag_score2[k];
score2 += diag_score2[j];
if ( score2 > best_score2 ) {
from = k + 1;
end = j;
best_score = score;
best_score2 = score2;
if( diag_score2[j] > max_diag2 ){
max_diag2 = diag_score2[j];
max_diag = diag_score[j];
imax_diag = j;
}
}
}
int mlen = imax_diag;
if( imax_diag > len1 ) mlen = nall - imax_diag;
int emax = int((1.0 - options.cluster_thd) * mlen) + 1;
for (j=from; j<imax_diag; j++) { // if aap pairs fail to open gap
if ( (imax_diag - j) > emax || diag_score[j] < 1 ) {
best_score -= diag_score[j]; from++;
} else break;
}
for (j=end; j>imax_diag; j--) { // if aap pairs fail to open gap
if ( (j - imax_diag) > emax || diag_score[j] < 1 ) {
best_score -= diag_score[j]; end--;
} else break;
}
// delete [] diag_score;
band_left = from - len1 + 1;
band_right= end - len1 + 1;
band_center = imax_diag - len1 + 1;
best_sum = best_score;
return OK_FUNC;
}
// END diag_test_aapn
int diag_test_aapn_est(int NAA1, char iseq2[], int len1, int len2, WorkingBuffer & buffer,
int &best_sum, int band_width, int &band_left, int &band_center, int &band_right, int required_aa1)
{
int i, i1, j, k;
int *pp, *pp2;
int nall = len1+len2-1;
int NAA2 = NAA1 * NAA1;
int NAA3 = NAA2 * NAA1;
Vector<int> & taap = buffer.taap;
Vector<INTs> & aap_begin = buffer.aap_begin;
Vector<INTs> & aap_list = buffer.aap_list;
Vector<int> & diag_score = buffer.diag_score;
Vector<int> & diag_score2 = buffer.diag_score2;
if (nall > MAX_DIAG) bomb_error("in diag_test_aapn_est, MAX_DIAG reached");
pp = & diag_score[0];
pp2 = & diag_score2[0];
for (i=nall; i; i--, pp++, pp2++) *pp = *pp2 =0;
INTs *bip;
int c22, cpx;
int len22 = len2-3;
i1 = len1-1;
for (i=0; i<len22; i++,i1++,iseq2++) {
unsigned char c0 = iseq2[0];
unsigned char c1 = iseq2[1];
unsigned char c2 = iseq2[2];
unsigned char c3 = iseq2[3];
if ((c0>=4) || (c1>=4) || (c2>=4) || (c3>=4)) continue; //skip N
c22 = c0*NAA3+ c1*NAA2 + c2*NAA1 + c3;
if ( (j=taap[c22]) == 0) continue;
cpx = 1 + (c0 != c1) + (c1 != c2) + (c2 != c3);
bip = & aap_list[ aap_begin[c22] ]; // bi = aap_begin[c22];
for (; j; j--, bip++) {
diag_score[i1 - *bip]++;
diag_score2[i1 - *bip] += cpx;
}
}
#if 0
int mmax = 0;
int immax = 0;
for(i=0; i<=nall; i++){
if( i%len2 ==0 or i == nall ) printf( "\n" );
printf( "%3i ", diag_score[i] );
if( diag_score[i] > mmax ){
mmax = diag_score[i];
immax = i;
}
}
#endif
//find the best band range
// int band_b = required_aa1;
int band_b = required_aa1-1 >= 0 ? required_aa1-1:0; // on dec 21 2001
int band_e = nall - band_b;
if( options.is454 ){
band_b = len1 - band_width;
band_e = len1 + band_width;
if( band_b < 0 ) band_b = 0;
if( band_e > nall ) band_e = nall;
}
int band_m = ( band_b+band_width-1 < band_e ) ? band_b+band_width-1 : band_e;
int best_score=0;
int best_score2=0;
int max_diag = 0;
int max_diag2 = 0;
int imax_diag = 0;
for (i=band_b; i<=band_m; i++){
best_score += diag_score[i];
best_score2 += diag_score2[i];
if( diag_score2[i] > max_diag2 ){
max_diag2 = diag_score2[i];
max_diag = diag_score[i];
imax_diag = i;
}
}
int from=band_b;
int end =band_m;
int score = best_score;
int score2 = best_score2;
for (k=from, j=band_m+1; j<band_e; j++, k++) {
score -= diag_score[k];
score += diag_score[j];
score2 -= diag_score2[k];
score2 += diag_score2[j];
if ( score2 > best_score2 ) {
from = k + 1;
end = j;
best_score = score;
best_score2 = score2;
if( diag_score2[j] > max_diag2 ){
max_diag2 = diag_score2[j];
max_diag = diag_score[j];
imax_diag = j;
}
}
}
#if 0
printf( "%i %i\n", required_aa1, from );
printf( "max=%3i imax=%3i; band: %3i %3i %i\n", max_diag, imax_diag, band_b, band_e, band_m );
printf( "best: %i\n", best_score );
printf( "from: %i, end: %i, best: %i\n", from, end, best_score );
#endif
int mlen = imax_diag;
if( imax_diag > len1 ) mlen = nall - imax_diag;
int emax = int((1.0 - options.cluster_thd) * mlen) + 1;
for (j=from; j<imax_diag; j++) { // if aap pairs fail to open gap
if ( (imax_diag - j) > emax || diag_score[j] < 1 ) {
best_score -= diag_score[j]; from++;
} else break;
}
for (j=end; j>imax_diag; j--) { // if aap pairs fail to open gap
if ( (j - imax_diag) > emax || diag_score[j] < 1 ) {
best_score -= diag_score[j]; end--;
} else break;
}
band_left = from-len1+1;
band_right= end-len1+1;
band_center = imax_diag - len1 + 1;
best_sum = best_score;
if( options.is454 ){
if( band_left > 0 ) best_sum = 0;
if( band_right < 0 ) best_sum = 0;
}
#if 0
printf( "%3i: best: %i, %i %i %i\n", required_aa1, best_score, band_left, band_right, band_width );
printf( "max=%3i imax=%3i; band: %3i %3i %i\n", mmax, immax, band_b, band_e, band_m );
#endif
return OK_FUNC;
}
// END diag_test_aapn_est
/*
local alignment of two sequence within a diag band
for band 0 means direction (0,0) -> (1,1)
1 means direction (0,1) -> (1,2)
-1 means direction (1,0) -> (2,1)
added on 2006 11 13
band 0 XXXXXXXXXXXXXXXXXX seq2, rep seq
XXXXXXXXXXXXXXX seq1
band 1 XXXXXXXXXXXXXXXXXX seq2, rep seq
XXXXXXXXXXXXXXX seq1
extreme right (+) XXXXXXXXXXXXXXXXXX seq2, rep seq
band = len2-1 XXXXXXXXXXXXXXX seq1
band-1 XXXXXXXXXXXXXXXXXX seq2, rep seq
XXXXXXXXXXXXXXX seq1
extreme left (-) XXXXXXXXXXXXXXXXXX seq2, rep seq
XXXXXXXXXXXXXXX band = -(len1-1) seq1
iseq len are integer sequence and its length,
mat is matrix, return ALN_PAIR class
band: -101 seq2 len2 = 17
\\\1234567890123456
0 \xxxxxxxxxxxxxxxxx
1 xxxxxxxxxxxxxxxxx\ most right band = len2-1
2 xxxxxxxxxxxxxxxxx
seq1 3 xxxxxxxxxxxxxxxxx
len1 = 11 4 xxxxxxxxxxxxxxxxx
5 xxxxxxxxxxxxxxxxx
6 xxxxxxxxxxxxxxxxx
7 xxxxxxxxxxxxxxxxx
8 xxxxxxxxxxxxxxxxx
9 xxxxxxxxxxxxxxxxx
0 xxxxxxxxxxxxxxxxx
\
most left band = -(len1-1)
*/
int local_band_align( char iseq1[], char iseq2[], int len1, int len2, ScoreMatrix &mat,
int &best_score, int &iden_no, int &alnln, float &dist, int *alninfo,
int band_left, int band_center, int band_right, WorkingBuffer & buffer)
{
int i, j, k, j1;
int jj, kk;
int iden_no1;
int64_t best_score1;
iden_no = 0;
if ( (band_right >= len2 ) ||
(band_left <= -len1) ||
(band_left > band_right) ) return FAILED_FUNC;
// allocate mem for score_mat[len1][len2] etc
int band_width = band_right - band_left + 1;
int band_width1 = band_width + 1;
// score_mat, back_mat [i][j]: i index of seqi (0 to len(seqi)-1), j index of band (0 to band_width-1)
MatrixInt64 & score_mat = buffer.score_mat;
MatrixInt & back_mat = buffer.back_mat;
//printf( "%i %i\n", band_right, band_left );
if( score_mat.size() <= len1 ){
VectorInt row( band_width1, 0 );
VectorInt64 row2( band_width1, 0 );
while( score_mat.size() <= len1 ){
score_mat.Append( row2 );
back_mat.Append( row );
}
}
for(i=0; i<=len1; i++){
if( score_mat[i].Size() < band_width1 ) score_mat[i].Resize( band_width1 );
if( back_mat[i].Size() < band_width1 ) back_mat[i].Resize( band_width1 );
}
best_score = 0;
/* seq1 is query, seq2 is rep
seq2 len2 = 17 seq2 len2 = 17 seq2 len2 = 17
01234567890123456 01234567890123456 01234567890123456
0 xxxxxxxxxxxxxxxxx \\\\\\XXXxxxxxxxxxxxxxx xXXXXXXXxxxxxxxxx
1 \\\\\Xxxxxxxxxxxxxxxxx \\\\\Xxx\xxxxxxxxxxxxx xx\xxxxx\xxxxxxxx
2 \\\\X\xxxxxxxxxxxxxxx \\\\Xxxx\xxxxxxxxxxxx xxx\xxxxx\xxxxxxx
seq1 3 \\\Xx\xxxxxxxxxxxxxx \\\Xxxxx\xxxxxxxxxxx xxxx\xxxxx\xxxxxx
len1 4 \\Xxx\xxxxxxxxxxxxx \\Xxxxxx\xxxxxxxxxx xxxxx\xxxxx\xxxxx
= 11 5 \Xxxx\xxxxxxxxxxxx \Xxxxxxx\xxxxxxxxx xxxxxx\xxxxx\xxxx
6 Xxxxx\xxxxxxxxxxx Xxxxxxxx\xxxxxxxx xxxxxxx\xxxxx\xxx
7 x\xxxx\xxxxxxxxxx x\xxxxxxx\xxxxxxx xxxxxxxx\xxxxx\xx
8 xx\xxxx\xxxxxxxxx xx\xxxxxxx\xxxxxx xxxxxxxxx\xxxxx\x
9 xxx\xxxx\xxxxxxxx xxx\xxxxxxx\xxxxx xxxxxxxxxx\xxxxx\
0 xxxx\xxxx\xxxxxxx xxxx\xxxxxxx\xxxx xxxxxxxxxxx\xxxxx
band_left < 0 (-6) band_left < 0 (-6) band_left >=0 (1)
band_right < 0 (-1) band_right >=0 (2) band_right >=0(7)
band_width 6 band_width 9 band_width 7
init score_mat, and iden_mat (place with upper 'X')
*/
if (band_left < 0) { //set score to left border of the matrix within band
int tband = (band_right < 0) ? band_right : 0;
//for (k=band_left; k<tband; k++)
for (k=band_left; k<=tband; k++) { // fixed on 2006 11 14
i = -k;
j1 = k-band_left;
// penalty for leading gap opening = penalty for gap extension
// each of the left side query hunging residues give ext_gap (-1)
score_mat[i][j1] = mat.ext_gap * i;
back_mat[i][j1] = DP_BACK_TOP;
}
back_mat[-tband][tband-band_left] = DP_BACK_NONE;
}
if (band_right >=0) { //set score to top border of the matrix within band
int tband = (band_left > 0) ? band_left : 0;
for (j=tband; j<=band_right; j++) {
j1 = j-band_left;
score_mat[0][j1] = mat.ext_gap * j;
back_mat[0][j1] = DP_BACK_LEFT;
}
back_mat[0][tband-band_left] = DP_BACK_NONE;
}
int gap_open[2] = { mat.gap, mat.ext_gap };
int max_diag = band_center - band_left;
int extra_score[4] = { 4, 3, 2, 1 };
for (i=1; i<=len1; i++) {
int J0 = 1 - band_left - i;
int J1 = len2 - band_left - i;
if( J0 < 0 ) J0 = 0;
if( J1 >= band_width ) J1 = band_width;
for (j1=J0; j1<=J1; j1++){
j = j1+i+band_left;
int ci = iseq1[i-1];
int cj = iseq2[j-1];
int sij = mat.matrix[ci][cj];
//int iden_ij = (ci == cj);
int s1, k0, back;
/* extra score according to the distance to the best diagonal */
int extra = extra_score[ abs(j1 - max_diag) & 3 ]; // max distance 3
sij += extra * (sij>0);
back = DP_BACK_LEFT_TOP;
best_score1 = score_mat[i-1][j1] + sij;
int gap0 = gap_open[ (i == len1) | (j == len2) ];
int gap = 0;
int64_t score;
if( j1 > 0 ){
gap = gap0;
if( back_mat[i][j1-1] == DP_BACK_LEFT ) gap = mat.ext_gap;
if( (score = score_mat[i][j1-1] + gap) > best_score1 ){
back = DP_BACK_LEFT;
best_score1 = score;
}
}
if(j1+1<band_width){
gap = gap0;
if( back_mat[i-1][j1+1] == DP_BACK_TOP ) gap = mat.ext_gap;
if( (score = score_mat[i-1][j1+1] + gap) > best_score1 ){
back = DP_BACK_TOP;
best_score1 = score;
}
}
score_mat[i][j1] = best_score1;
back_mat[i][j1] = back;
//printf( "%2i(%2i) ", best_score1, iden_no1 );
}
//printf( "\n" );
}
i = j = 0;
if( len2 - band_left < len1 ){
i = len2 - band_left;
j = len2;
}else if( len1 + band_right < len2 ){
i = len1;
j = len1 + band_right;
}else{
i = len1;
j = len2;
}
j1 = j - i - band_left;
best_score = score_mat[i][j1];
best_score1 = score_mat[i][j1];
#if 1
const char *letters = "acgtnx";
const char *letters2 = "ACGTNX";
#else
const char *letters = "arndcqeghilkmfpstwyvbzx";
const char *letters2 = "ARNDCQEGHILKMFPSTWYVBZX";
#endif
int back = back_mat[i][j1];
int last = back;
int count = 0, count2 = 0, count3 = 0;
int match, begin1, begin2, end1, end2;
int gbegin1=0, gbegin2=0, gend1=0, gend2=0;
int64_t score, smin = best_score1, smax = best_score1 - 1;
int posmin, posmax, pos = 0;
int bl, dlen = 0, dcount = 0;
posmin = posmax = 0;
begin1 = begin2 = end1 = end2 = 0;
#ifdef PRINT
#define PRINT
printf( "%i %i\n", best_score, score_mat[i][j1] );
printf( "%i %i %i\n", band_left, band_center, band_right );
printf( "%i %i %i %i\n", i, j, j1, len2 );
#endif
#ifdef MAKEALIGN
#define MAKEALIGN
char AA[ MAX_SEQ ], BB[ MAX_SEQ ];
int NN = 0;
int IA, IB;
for(IA=len1;IA>i;IA--){
AA[NN] = letters[ iseq1[IA-1] ];
BB[NN++] = '-';
}
for(IB=len2;IB>j;IB--){
AA[NN] = '-';
BB[NN++] = letters[ iseq2[IB-1] ];
}
#endif
int masked = 0;
int indels = 0;
int max_indels = 0;
while( back != DP_BACK_NONE ){
switch( back ){
case DP_BACK_TOP :
#ifdef PRINT
printf( "%5i: %c %c %9i\n", pos, letters[ iseq1[i-1] ], '|', score_mat[i][j1] );
#endif
#ifdef MAKEALIGN
AA[NN] = letters[ iseq1[i-1] ];
BB[NN++] = '-';
#endif
bl = (last != back) & (j != 1) & (j != len2);
dlen += bl;
dcount += bl;
score = score_mat[i][j1];
if( score < smin ){
count2 = 0;
smin = score;
posmin = pos - 1;
begin1 = i;
begin2 = j;
}
i -= 1;
j1 += 1;