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my_needle.cpp
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my_needle.cpp
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/* @funcstatic embAlignGetScoreNWMatrix ***************************************
**
** Returns score of the optimal global or overlap alignment for
** the specified path matrix for Needleman Wunsch
**
** @param [r] ix [const float*] Gap scores array, ix(i,j) is the best score
** given that a(i) is aligned to a gap
** (in an insertion with respect to b)
** @param [r] iy [const float*] Gap scores array, iy(i,j) is the best score
** given that b(i) is in an insertion
** with respect to a
**
** @param [r] m [const float*] Match scores array, m(i,j) is the best score
** up to (i,j) given that a(i) is aligned to b(j)
** @param [r] lena [ajint] length of the first sequence
** @param [r] lenb [ajint] length of the second sequence
** @param [w] start1 [ajint *] start of alignment in first sequence
** @param [w] start2 [ajint *] start of alignment in second sequence
** @param [r] endweight [AjBool] whether the matrix was built for
** a global or overlap alignment
**
** @return [float] optimal score
******************************************************************************/
/*
* =====================================================================================
* Filename: my_needle.cpp
* Description: global sequence alignment with position specific gap
* penalties
* Created: 09/09/2010 11:26:51 PM CEST
* Compiler: g++
* Author: Nanjiang Shu, [email protected]
* Company: Department of Biochemistry and Biophysics, Stockholm Univesity
* =====================================================================================
*/
#include <cstdio>
#include <sys/stat.h>
#include <sys/types.h>
#include <cstring>
#include <cctype>
#include <cstdlib>
#include <cmath>
#include <string>
#include <map>
#include <set>
#include <vector>
#include <iostream>
#include <sstream>
#include <fstream>
#include <algorithm>
#include <cassert>
#include <ctime>
#include <climits>
#include "array.h"
using namespace std;
typedef unsigned char BYTE;
struct Pair{/*{{{*/
string mem1;
string mem2;
};/*}}}*/
struct dbindex{/*{{{*/
int dbfileindex;
long offset;
unsigned long size;
};/*}}}*/
/*the gapopenarray,
* if want to open a gap at position 4, set the gapopen score at 4th position
* to be a low value
* e.g.
*
* ACDEGD
* AVDEGD
*
* if you want an alignment
* ACD-EGD
* AVDEGD-
*
* set the gapopen value of seq1 gapopen[3] = -1000
*
* */
#ifndef WHITE_SPACE
#define WHITE_SPACE " \t\r\n"
#endif
#ifndef SEQALIGN
#define SEQALIGN
/*for the alignment result*/
#define IDT 3 /* identity*/
#define SIM 2 /* similar, positive*/
#define MIS 1 /* mismatch*/
#define GAP 0 /* gap*/
#endif
#ifndef ERROR_CODE
#define READ_FILE_ERROR 1
#define WRITE_FILE_ERROR 2
//#define READ_OVERFLOW 5
//#define WRITE_OVERFLOW 5
//#define UNDERFLOW 10
#endif /*ERROR_CODE*/
#ifndef SEQ_TYPE
#define SEQ_TYPE
#define DNA_SEQ 0 // dna sequence
#define AA_SEQ 1 // amino acid sequence
#define SHAPE_SEQ 2 // shape string sequence
#define UNKNOWN_SEQ_TYPE -1
#endif
typedef int ajint;
typedef unsigned int ajuint;
typedef ajint AjBool;
typedef signed char int8;
#define ajFalse 0
#define ajTrue 1
#define U_FEPS 1.192e-6F /* 1.0F + E_FEPS != 1.0F */
#define U_DEPS 2.22e-15 /* 1.0 + E_DEPS != 1.0 */
#undef DIAG
#undef LEFT
#undef DOWN
#define DIAG 0
#define LEFT 1
#define DOWN 2
#undef CHAR_GAP
#define CHAR_GAP '-'
#define E_FPEQ(a,b,e) (((b - e) < a) && (a < (b + e)))
#undef SIZE_TITLE
#define SIZE_TITLE 100
#undef LONGEST_SEQ
int LONGEST_SEQ=80000;
float gapopen = 10.0;
float gapextend = 0.5;
float endgapopen = 10.0;
float endgapextend = 10.0;
int seq_type = AA_SEQ; /* sequence type, default is amino acid sequence*/
int nchar = 50; /*maximum length of sequence to print at each line*/
bool isCheckSeqIDTClass = true;
bool isShowProgress = true;
bool isRandSelection = true;
int method_select_pair = 1;
#define HIGH_COVERAGE 0
#define HIGH_PRECISION 1
int KMerThresholdMode = HIGH_PRECISION;
bool isPrintKMerBitScore = false;
int wordsize = 3;
int maxSeqIDTClass[]={
10000, /*0 - 10*/
10000, /*10 - 20*/
10000, /*20 - 30*/
10000, /*30 - 40*/
10000, /*40 - 50*/
10000, /*50 - 60*/
10000, /*60 - 70*/
10000, /*70 - 80*/
10000, /*80 - 90*/
10000 /*90 - 100*/
};
float binSeqIDTClass[] = {
0.0, 10.0,
10.0, 20.0,
20.0, 30.0,
30.0, 40.0,
40.0, 50.0,
50.0, 60.0,
60.0, 70.0,
70.0, 80.0,
80.0, 90.0,
90.0, 100.0
};
int numSeqIDTClass = sizeof(maxSeqIDTClass)/sizeof(int);
const int para20[]={
1,
20,
20*20,
20*20*20,
20*20*20*20,
20*20*20*20*20,
20*20*20*20*20*20,
20*20*20*20*20*20*20,
};
const int aacode[]=
{-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, /*first 65 chars*/
/*unique AA, ARNDCQEGHILKMFPSTWYVBZX */
/*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 */
0,20,4,3,6,13,7,8,9,22,11,10,12,2,22,14,5,1,15,16,22,19,17,22,18,21
-1,-1,-1,-1,-1,-1,-1,
/*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 */
0,20,4,3,6,13,7,8,9,22,11,10,12,2,22,14,5,1,15,16,22,19,17,22,18,21
};
#define NUM_BLOSUM 24 //size of BLOSUM matrix
#define NUM_NUC 15
#define NUM_SHAG 12
int MAX_ALIGN_SIZE=1024; /*1024 MB*/
int THRESHOLD_DB_FILESIZE = 0; /*0 MB*/
/* Experiments show that the most time consuming part is the alignment, not
* file reading. The gain by reading all sequences in to memory is very little.
* so just use fseek and fread technique.
*
$ /data3/program/my_needle/my_needle -mode 1 -l t3.pair -seqdb pfamfullseq_uniq.fasta -o t3.txt -threshold-seqdb-size 0 -m 1
# Read Database Index with 1393148 records costs 4.51 seconds.
# Align 3000 pairs of sequences costs 9.04 seconds.
/data3/program/my_needle/my_needle -mode 1 -l t3.pair -seqdb pfamfullseq_uniq.fasta -o t3.1.txt -threshold-seqdb-size 1024 -m 1
# GetIDSeqMap of 1393148 sequences costs 7.49 seconds.
# Align 3000 pairs of sequences costs 8.95 seconds.
*/
struct AlignFactor/*{{{*/
{
float score;
float zScore;
float pozScore;
double eValue;
int idt_cnt;
float identity;
float identity_short;
int sim_cnt;
float similarity;
float similarity_short;
int gap_cnt;
float gapPercent;
};/*}}}*/
const char ALPHABET_BLOSUM[]="ARNDCQEGHILKMFPSTWYVBZX*";
const char ALPHABET_NUC[]="ATGCSWRYKMBVHDN";
const char ALPHABET_SHAG[]="AKRSUVTGHBC-";
int outformat = 0; /*set by the -m option
0: full pairwise alignment
1: full pairwise alignment in Fasta format, they are placed sequentially */
int pairlistmode=0;/*set by the -mode option
0: pairs are two filenames of sequences
1: pairs are two seqIDs of sequences
2: all-to-all alignment given a file with multiple sequences
*/
const int blosum62[][NUM_BLOSUM] =/*{{{*/
{ // substitution matrix for amino acid sequences
/* A R N D C Q E G H I L K M F P S T W Y V B Z X * */
{ 4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3, -2, 0, -2, -1, 0, -4},
{ -1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2, -3, -1, 0, -1, -4},
{ -2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3, 3, 0, -1, -4},
{ -2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4, -3, -3, 4, 1, -1, -4},
{ 0, -3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2, -2, -1, -3, -3, -2, -4},
{ -1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1, -2, 0, 3, -1, -4},
{ -1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1, -4},
{ 0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2, -3, -3, -1, -2, -1, -4},
{ -2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2, -3, 0, 0, -1, -4},
{ -1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3, -1, 3, -3, -3, -1, -4},
{ -1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2, -1, 1, -4, -3, -1, -4},
{ -1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2, -2, 0, 1, -1, -4},
{ -1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1, -1, 1, -3, -1, -1, -4},
{ -2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3, -1, -3, -3, -1, -4},
{ -1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1, -4, -3, -2, -2, -1, -2, -4},
{ 1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2, -2, 0, 0, 0, -4},
{ 0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2, -2, 0, -1, -1, 0, -4},
{ -3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2, 11, 2, -3, -4, -3, -2, -4},
{ -2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2, 7, -1, -3, -2, -1, -4},
{ 0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3, -1, 4, -3, -2, -1, -4},
{ -2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4, -3, -3, 4, 1, -1, -4},
{ -1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1, -4},
{ 0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0, -2, -1, -1, -1, -1, -1, -4},
{ -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, 1}
};
/*}}}*/
const int nuc44[][NUM_NUC] =/*{{{*/
{ // substitution matrix for DNA
//# This matrix was created by Todd Lowe 12/10/92
//# Uses ambiguous nucleotide codes, probabilities rounded to nearest integer
//# Lowest score = -4, Highest score = 5
//A T G C S W R Y K M B V H D N
{ 5, -4 , -4 , -4 , -4 , 1 , 1 , -4 , -4 , 1 , -4 , -1 , -1 , -1 , -2 },
{-4, 5 , -4 , -4 , -4 , 1 , -4 , 1 , 1 , -4 , -1 , -4 , -1 , -1 , -2 },
{-4, -4 , 5 , -4 , 1 , -4 , 1 , -4 , 1 , -4 , -1 , -1 , -4 , -1 , -2 },
{-4, -4 , -4 , 5 , 1 , -4 , -4 , 1 , -4 , 1 , -1 , -1 , -1 , -4 , -2 },
{-4, -4 , 1 , 1 , -1 , -4 , -2 , -2 , -2 , -2 , -1 , -1 , -3 , -3 , -1 },
{ 1, 1 , -4 , -4 , -4 , -1 , -2 , -2 , -2 , -2 , -3 , -3 , -1 , -1 , -1 },
{ 1, -4 , 1 , -4 , -2 , -2 , -1 , -4 , -2 , -2 , -3 , -1 , -3 , -1 , -1 },
{-4, 1 , -4 , 1 , -2 , -2 , -4 , -1 , -2 , -2 , -1 , -3 , -1 , -3 , -1 },
{-4, 1 , 1 , -4 , -2 , -2 , -2 , -2 , -1 , -4 , -1 , -3 , -3 , -1 , -1 },
{ 1, -4 , -4 , 1 , -2 , -2 , -2 , -2 , -4 , -1 , -3 , -1 , -1 , -3 , -1 },
{-4, -1 , -1 , -1 , -1 , -3 , -3 , -1 , -1 , -3 , -1 , -2 , -2 , -2 , -1 },
{-1, -4 , -1 , -1 , -1 , -3 , -1 , -3 , -3 , -1 , -2 , -1 , -2 , -2 , -1 },
{-1, -1 , -4 , -1 , -3 , -1 , -3 , -1 , -3 , -1 , -2 , -2 , -1 , -2 , -1 },
{-1, -1 , -1 , -4 , -3 , -1 , -1 , -3 , -1 , -3 , -2 , -2 , -2 , -1 , -1 },
{-2, -2 , -2 , -2 , -1 , -1 , -1 , -1 , -1 , -1 , -1 , -1 , -1 , -1 , -1 }
};/*}}}*/
const int shag6[][NUM_SHAG] =/*{{{*/
{ // substitution matrix for shape strings
//# substitution matrix in integer format, scale = 9
//# modified on 2007-03-18,
//# the score of A-K should be positive and U-V as well
//# in that case, manually modify
//# A-A = 3
//# A-K = 2
//# A-U/V = 1
//# K-U/V = 1
//# R-S = 1
//# R-U/V = 1
// A K R S U V T G H B C -
{ 3, 2,-4, -6, 1, 1, -2, -3, 2, -5, -3, -1, },
{ 2, 5,-1, -3, 1, 1, 0, 0, 1, -2, 1, 0, },
{-4,-1, 4, 1, 1, 1, -1, 0, -3, 2, 0, 0, },
{-6,-3, 1, 4, 1, 1, -3, 0, -6, 3, -1, -1, },
{ 1, 1, 1, 1, 9, 5, 1, 1, -2, 0, 4, 0, },
{ 1, 1, 1, 1, 5, 8, 1, 0, -2, 1, 4, 0, },
{-2, 0,-1, -3, 1, 1, 9, 2, -2, -2, 7, 0, },
{-3, 0, 0, 0, 1, 0, 2, 11, -2, 0, 6, 0, },
{ 2, 1,-3, -6, -2, -2, -2, -2, 2, -5, -2, -1, },
{-5,-2, 2, 3, 0, 1, -2, 0, -5, 3, -1, 0, },
{-3, 1, 0, -1, 4, 4, 7, 6, -2, -1, 6, 0, },
{-1, 0, 0, -1, 0, 0, 0, 0, -1, 0, 0, 0, }
};/*}}}*/
char alphabet[500] = "";
AjBool endweight = false;
bool show = false;
string matrixFile = "";
int sizeAlphabet = 0;
bool isPrintTraceMatrix = false;
bool noGapOpenArray = false;
int alnType = AA_SEQ;
char usage[]/*{{{*/="\n\
usage: my_needle [options] seqfile1 seqfile2\n\
\n\
Pairwise sequence alignment derived from the needle program in the EMBOSS package\n\
Gapopens can be supplied under the sequence and enclosed in { }\n\
\n\
Options:\n\
-list FILE Supply the pair list, one line a pair\n\
-mode INT Pair mode, (default: 0)\n\
0: pairs are two filenames of sequences\n\
1: pairs are two seqIDs of sequences\n\
2: do all-to-all pairwise alignment given a fasta file\n\
with multiple sequences\n\
-seqdb STR Indexed sequence database, this must be supplied when mode = 1\n\
-m INT Output alignment format, (default: 0)\n\
0: full pairwise alignment in EMBOSS needle format\n\
1: full pairwise alignment in Fasta format\n\
-table FILE Output tab delimited alignment info table to FILE\n\
-type INT Set the alignment type. (default: 1)\n\
0: for dna, \n\
1: for aaseq\n\
2: for shape strings\n\
-matrix FILE Supply substitution matrix file. default is\n\
NUC.4.4: for DNA alignment\n\
BLOSUM62: for amino acid alignment\n\
ShagMatrix6: for shape string alignment\n\
-title1 STR Force the title of the first seqfile\n\
-title2 STR Force the title of the second seqfile\n\
-G FLOAT Penalty to open a gap, (default: 10.0)\n\
-E FLOAT Penalty to extend a gap, default: 0.5)\n\
-o FILE Output the alignment to outfile, (default: stdout)\n\
-eg FLOAT Set endgapopen, (default: 10.0)\n\
-ee FLOAT Set endgapextend, (default: 0.5)\n\
-debug FILE Print the debug information to FILE\n\
-endweight Enable endweight, default= No\n\
-nogoarray Do not use the gapopen array even supplied\n\
-threshold-seqdb-size INT\n\
Threshold of seqdb file size in MB. (default: 1024)\n\
If seqdb filesize < threshold, the whole file will be read\n\
in to memory.\n\
-max-align-size INT\n\
Maximum align size in MB. (default: 1024)\n\
max_align_size = seqlength1 * seqlengh2\n\
-selpair INT Pair selection method for mode 2, (default: 1)\n\
0: sequentially \n\
1: randomly\n\
-wordsize INT Wordsize for Kmer comparison, (default: 3)\n\
-pkmer|-printkmerscore yes|no\n\
Whether print KMer score, (default: no)\n\
\n\
-h | --help Print this help message and exit\n\
\n\
Created on 2010-09-10, updated 2012-05-30, Nanjiang\n\
\n\
Examples:\n\
# align the first sequence in test1.fa to all sequences in the test2.fa\n\
my_needle test1.fa test2.fa\n\
\n\
# align a large number of pairs of sequences by supplying sequence db and\n\
# pairs of seqids\n\
my_needle -list pairlist.txt -mode 1 -seqdb seqdb -m 1 -o outfile.txt\n\
\n\
# all to all pairwise alignment given a file with multiple sequences\n\
my_needle t2.fa -mode 2 -m 1 -table table1.txt\n\
";
/*}}}*/
char explanation_table_format[]="\
# Seq1 Sequence 1 in alignment\n\
# Seq2 Sequence 2 in alignment\n\
# IDT0 numIDTRes / alnLength\n\
# SIM0 numSIMRes / alnLength\n\
# AlnLength length of the alignment\n\
# Len1 length of sequence 1 in the pair\n\
# Len2 length of sequence 2 in the pair\n\
# Score alignment score\n\
# N_IDT number of identical residues\n\
# N_SIM number of similar (including identical) residues\n\
# N_GAP number of gaps\n\
# IDT1 numIDTRes / min(len1, len2)\n\
# IDT2 numIDTRes / (alnLength - N_GAP)\n\
#\n";
void PrintHelp() {/*{{{*/
fprintf(stdout,"%s\n",usage);
} /*}}}*/
void PrintNeedleAlignmentHeader(string &programname,struct tm* timeinfo,string& outfile, int argc, char **argv,FILE *fpout)/*{{{*/
{
fprintf(fpout,"########################################\n");
fprintf(fpout,"# Program: %s\n", programname.c_str());
fprintf(fpout,"# Rundate: %s", asctime(timeinfo));
fprintf(fpout,"# Commandline: ");
for (int jj = 0; jj < argc; jj++) {
fprintf(fpout,"%s ", argv[jj]);
}
fprintf(fpout,"\n");
fprintf(fpout,"# Align_format: %s\n", "srspair");
fprintf(fpout,"# Report_file: %s\n", outfile.c_str());
fprintf(fpout,"########################################\n");
fprintf(fpout,"\n");
}/*}}}*/
bool IsFileExist(const char *name)/*{{{*/
{
struct stat st;
return (stat(name,&st) == 0);
}/*}}}*/
bool IsInCharSet(const char ch, const char *charSet, int n /*= 0 */)/*{{{*/
/*****************************************************************************
* check if the character "ch" is in charSet,
****************************************************************************/
{
if(n == 0) {
n = strlen(charSet);
}
int i;
for(i = 0 ;i < n ; i ++) {
if(ch == charSet[i]) {
return true;
}
}
return false;
}/*}}}*/
int GetFileSize(const char *name)/*{{{*/
{
struct stat st;
if (stat(name,&st) == 0){
return st.st_size;
}else{
cerr << "File "
<< name
<< " does not exist." << endl;
return -1;
}
}/*}}}*/
string int2string(int number)/*{{{*/
{
stringstream ss;//create a stringstream
ss << number;//add number to the stream
return ss.str();//return a string with the contents of the stream
}/*}}}*/
void InitAlignFactor(AlignFactor *pAlignFactor)/*{{{*/
{
pAlignFactor -> score = 0.0;
pAlignFactor -> zScore = 0.0;
pAlignFactor -> pozScore = 0.0;
pAlignFactor -> eValue = 0.0;
pAlignFactor -> idt_cnt = 0;
pAlignFactor -> identity = 0.0;
pAlignFactor -> identity_short = 0.0;
pAlignFactor -> sim_cnt = 0;
pAlignFactor -> similarity = 0.0;
pAlignFactor -> similarity_short = 0.0;
pAlignFactor -> gap_cnt = 0;
pAlignFactor -> gapPercent = 0.0;
}
/*}}}*/
bool IsAllGroupFilled(vector <int> &cntSeqIDTClass)/*{{{*/
{
for (int i = 0 ; i < numSeqIDTClass ; i ++) {
if (cntSeqIDTClass[i] < maxSeqIDTClass[i]){
return false;
}
}
return true;
}
/*}}}*/
int GetSeqIDTClass(float seqIdentity, float* binSeqIDTClass, int numSeqIDTClass){/*{{{*/
for (int i = 0; i < numSeqIDTClass; i++){
//printf("%g %.3g %g\n", binSeqIDTClass[i], seqIdentity, binSeqIDTClass[i+1]);
if (seqIdentity >= binSeqIDTClass[2*i] && seqIdentity < binSeqIDTClass[2*i+1]){
return i;
}
}
return numSeqIDTClass;
}/*}}}*/
float GetThresholdKMerScore(float minimalSeqIdentity){/*{{{*/
/*sequence pair with kMerBitScore < threshold_kmerScore are not likely to
* have sequence identity > minimalSeqIdentity*/
/*To be developed*/
if (KMerThresholdMode == HIGH_COVERAGE ){
if (minimalSeqIdentity >=95.0){
return -0.3;
} else if (minimalSeqIdentity>=90.0){
return -0.5;
} else if (minimalSeqIdentity>=80.0){
return -1.0;
}else if (minimalSeqIdentity>=70.0){
return -1.3;
}else if (minimalSeqIdentity>=60.0){
return -1.5;
}else if (minimalSeqIdentity>=50.0){
return -1.6;
}else if (minimalSeqIdentity>=40.0){
return -1.8;
}else if (minimalSeqIdentity>=30.0){
return -2.0;
} else if (minimalSeqIdentity>=20.0){
return -2.2;
}else if (minimalSeqIdentity>=10.0) {
return -2.25;
}else{
return -99999.0;
}
}else{/*high precision*/
if (minimalSeqIdentity >=95.0){
return -0.25;
} else if (minimalSeqIdentity>=90.0){
return -0.4;
} else if (minimalSeqIdentity>=80.0){
return -0.75;
}else if (minimalSeqIdentity>=70.0){
return -1.2;
}else if (minimalSeqIdentity>=60.0){
return -1.4;
}else if (minimalSeqIdentity>=50.0){
return -1.5;
}else if (minimalSeqIdentity>=40.0){
return -1.6;
}else if (minimalSeqIdentity>=30.0){
return -1.75;
} else if (minimalSeqIdentity>=20.0){
return -1.75;
}else if (minimalSeqIdentity>=10.0) {
return -1.8;
}else{
return -99999.0;
}
}
}/*}}}*/
float GetMinimalSeqIdentity(vector <int> &cntSeqIDTClass, int *maxSeqIDTClass, float* binSeqIDTClass, int numSeqIDTClass){/*{{{*/
for (int i = 0; i < numSeqIDTClass; i++){
if (cntSeqIDTClass[i] < maxSeqIDTClass[i]){
return binSeqIDTClass[2*i];
}
}
return binSeqIDTClass[(numSeqIDTClass-1)*2+1];
}/*}}}*/
struct cmp_str/*{{{*/
{
bool operator()(char const *a, char const *b)
{
return std::strcmp(a, b) < 0;
}
};/*}}}*/
int CountKMerOfSequence_c(const char* seq, map <char*, int, cmp_str> &wordCountMap, int wordsize){/*{{{*/
/*c style*/
int len = strlen(seq);
map <char*,int, cmp_str> :: iterator it;
int i = 0;
while (i < len - wordsize + 1 ){
char *substr=new char[wordsize+1];
strncpy(substr,seq+i,wordsize);
substr[wordsize]='\0';
it = wordCountMap.find(substr);
if (it == wordCountMap.end()){
wordCountMap.insert(pair<char*, int > (substr, 1));
}else {
it->second += 1;
delete [] substr;
}
i++;
}
return wordCountMap.size();
}/*}}}*/
float CalKMerVectorScore_norm_c(map <char*, int, cmp_str> &wordCountMap1, map <char*, int, cmp_str> &wordCountMap2){/*{{{*/
float bitScore = 0.0;
float numWord1 = (float)wordCountMap1.size();
float numWord2 = (float)wordCountMap2.size();
set <char*, cmp_str> unionKeys;
map <char*, int, cmp_str> :: iterator it;
map <char*, int, cmp_str> :: iterator it1;
map <char*, int, cmp_str> :: iterator it2;
for (it = wordCountMap1.begin(); it != wordCountMap1.end(); it++){
unionKeys.insert(it->first);
}
for (it = wordCountMap2.begin(); it != wordCountMap2.end(); it++){
unionKeys.insert(it->first);
}
set <char*, cmp_str> ::iterator iss;
for (iss = unionKeys.begin(); iss != unionKeys.end(); iss++){
it1 = wordCountMap1.find(*iss) ;
it2 = wordCountMap2.find(*iss) ;
if (it1 != wordCountMap1.end() && it2 != wordCountMap2.end()){
bitScore -= fabs(it1->second/numWord1 - it2->second/numWord2);
}else {
if (it1 != wordCountMap1.end()){
bitScore -= it1 -> second/numWord1;
}else{
bitScore -= it2 -> second/numWord2;
}
}
}
return bitScore;
}/*}}}*/
void PrintKMerVectorPair_c(map <char*, int, cmp_str> &wordCountMap1, map <char*, int, cmp_str>& wordCountMap2, const char* id1, const char* id2, FILE *fpout) {/*{{{*/
set <char*, cmp_str> unionKeys;
map <char*, int, cmp_str> :: iterator it;
for (it = wordCountMap1.begin(); it != wordCountMap1.end(); it++){
unionKeys.insert(it->first);
}
for (it = wordCountMap2.begin(); it != wordCountMap2.end(); it++){
unionKeys.insert(it->first);
}
set <char*, cmp_str> ::iterator iss;
fprintf(fpout, "\n%13s%10s%13s %d (%d - %d)\n", id1, "", id2, (int)unionKeys.size(), (int)wordCountMap1.size(), (int)wordCountMap2.size());
for (iss = unionKeys.begin(); iss != unionKeys.end(); iss++){
it = wordCountMap1.find(*iss) ;
if (it != wordCountMap1.end()){
fprintf(fpout,"%6s %6d", (*iss), it->second);
}else {
fprintf(fpout,"%6s %6s", (*iss), "NULL");
}
fprintf(fpout, "%10s","");
it = wordCountMap2.find(*iss) ;
if (it != wordCountMap2.end()){
fprintf(fpout,"%6s %6d", (*iss), it -> second);
}else {
fprintf(fpout,"%6s %6s", (*iss), "NULL");
}
fprintf(fpout,"\n");
}
}/*}}}*/
void FreeMem_WrodMap_c(map <char*, int, cmp_str> &wordCountMap){/*{{{*/
map <char*, int> :: iterator it;
for (it = wordCountMap.begin(); it != wordCountMap.end(); it++){
delete [] it->first;
}
}/*}}}*/
float KMerVectorPairwiseComparison_c(string& seq1, string& seq2, string& seqID1, string& seqID2, int wordsize, FILE *fpLog){/*{{{*/
/*c style*/
map <char*, int, cmp_str> wordCountMap1;
map <char*, int, cmp_str> wordCountMap2;
CountKMerOfSequence_c(seq1.c_str(), wordCountMap1, wordsize);
CountKMerOfSequence_c(seq2.c_str(), wordCountMap2, wordsize);
#ifdef DEBUG_KMER
PrintKMerVectorPair_c(wordCountMap1, wordCountMap2, seqID1.c_str(), seqID2.c_str(), stdout);
#endif
float bitScore = CalKMerVectorScore_norm_c(wordCountMap1, wordCountMap2);
FreeMem_WrodMap_c(wordCountMap1);
FreeMem_WrodMap_c(wordCountMap2);
return bitScore;
}/*}}}*/
int CountKMerOfSequence(string &seq, map <string, int> &wordCountMap, int wordsize){/*{{{*/
int len = seq.size();
map <string,int> :: iterator it;
string substr;
for (int i=0;i < len-wordsize+1; i ++){
substr = seq.substr(i,wordsize);
it = wordCountMap.find(substr);
if (it == wordCountMap.end()){
wordCountMap.insert(pair<string, int> (substr, 1));
}else {
it->second += 1;
}
}
return wordCountMap.size();
}/*}}}*/
void PrintKMerVectorPair(map <string, int> &wordCountMap1, map <string, int>& wordCountMap2, string &id1, string&id2, FILE *fpout) {/*{{{*/
set <string> unionKeys;
map <string, int> :: iterator it;
for (it = wordCountMap1.begin(); it != wordCountMap1.end(); it++){
unionKeys.insert(it->first);
}
for (it = wordCountMap2.begin(); it != wordCountMap2.end(); it++){
unionKeys.insert(it->first);
}
set <string> ::iterator iss;
fprintf(fpout, "\n%13s%10s%13s %d (%d - %d)\n", id1.c_str(), "", id2.c_str(), (int)unionKeys.size(), (int)wordCountMap1.size(), (int)wordCountMap2.size());
for (iss = unionKeys.begin(); iss != unionKeys.end(); iss++){
it = wordCountMap1.find(*iss) ;
if (it != wordCountMap1.end()){
fprintf(fpout,"%6s %6d", (*iss).c_str(), it->second);
}else {
fprintf(fpout,"%6s %6s", (*iss).c_str(), "NULL");
}
fprintf(fpout, "%10s","");
it = wordCountMap2.find(*iss) ;
if (it != wordCountMap2.end()){
fprintf(fpout,"%6s %6d", (*iss).c_str(), it -> second);
}else {
fprintf(fpout,"%6s %6s", (*iss).c_str(), "NULL");
}
fprintf(fpout,"\n");
}
}/*}}}*/
float CalKMerVectorScore_old1(map <string, int> &wordCountMap1, map <string, int> &wordCountMap2){/*{{{*/
float bitScore = 0.0;
set <string> unionKeys;
map <string, int> :: iterator it;
map <string, int> :: iterator it1;
map <string, int> :: iterator it2;
for (it = wordCountMap1.begin(); it != wordCountMap1.end(); it++){
unionKeys.insert(it->first);
}
for (it = wordCountMap2.begin(); it != wordCountMap2.end(); it++){
unionKeys.insert(it->first);
}
set <string> ::iterator iss;
for (iss = unionKeys.begin(); iss != unionKeys.end(); iss++){
it1 = wordCountMap1.find(*iss) ;
it2 = wordCountMap2.find(*iss) ;
if (it1 != wordCountMap1.end() && it2 != wordCountMap2.end()){
bitScore += min(it1->second, it2->second);
}else {
if (it1 != wordCountMap1.end()){
bitScore -= it1 -> second;
}else{
bitScore -= it2 -> second;
}
}
}
return bitScore;
}/*}}}*/
float CalKMerVectorScore(map <string, int> &wordCountMap1, map <string, int> &wordCountMap2){/*{{{*/
float bitScore = 0.0;
set <string> unionKeys;
map <string, int> :: iterator it;
map <string, int> :: iterator it1;
map <string, int> :: iterator it2;
for (it = wordCountMap1.begin(); it != wordCountMap1.end(); it++){
unionKeys.insert(it->first);
}
for (it = wordCountMap2.begin(); it != wordCountMap2.end(); it++){
unionKeys.insert(it->first);
}
set <string> ::iterator iss;
for (iss = unionKeys.begin(); iss != unionKeys.end(); iss++){
it1 = wordCountMap1.find(*iss) ;
it2 = wordCountMap2.find(*iss) ;
if (it1 != wordCountMap1.end() && it2 != wordCountMap2.end()){
bitScore -= abs(it1->second - it2->second);
}else {
if (it1 != wordCountMap1.end()){
bitScore -= it1 -> second;
}else{
bitScore -= it2 -> second;
}
}
}
return bitScore;
}/*}}}*/
float CalKMerVectorScore_norm(map <string, int> &wordCountMap1, map <string, int> &wordCountMap2){/*{{{*/
float bitScore = 0.0;
float numWord1 = (float)wordCountMap1.size();
float numWord2 = (float)wordCountMap2.size();
set <string> unionKeys;
map <string, int> :: iterator it;
map <string, int> :: iterator it1;
map <string, int> :: iterator it2;
for (it = wordCountMap1.begin(); it != wordCountMap1.end(); it++){
unionKeys.insert(it->first);
}
for (it = wordCountMap2.begin(); it != wordCountMap2.end(); it++){
unionKeys.insert(it->first);
}
set <string> ::iterator iss;
for (iss = unionKeys.begin(); iss != unionKeys.end(); iss++){
it1 = wordCountMap1.find(*iss) ;
it2 = wordCountMap2.find(*iss) ;
if (it1 != wordCountMap1.end() && it2 != wordCountMap2.end()){
bitScore -= fabs(it1->second/numWord1 - it2->second/numWord2);
}else {
if (it1 != wordCountMap1.end()){
bitScore -= it1 -> second/numWord1;
}else{
bitScore -= it2 -> second/numWord2;
}
}
}
return bitScore;
}/*}}}*/
float KMerVectorPairwiseComparison(string& seq1, string& seq2, string& seqID1, string& seqID2, int wordsize, FILE *fpLog){/*{{{*/
map <string, int> wordCountMap1;
map <string, int> wordCountMap2;
CountKMerOfSequence(seq1, wordCountMap1, wordsize);
CountKMerOfSequence(seq2, wordCountMap2, wordsize);
#ifdef DEBUG_KMER
PrintKMerVectorPair(wordCountMap1, wordCountMap2, seqID1, seqID2, stdout);
#endif
//return 0.0;
//float bitScore = CalKMerVectorScore(wordCountMap1, wordCountMap2);
float bitScore = CalKMerVectorScore_norm(wordCountMap1, wordCountMap2);
//bitScore = bitScore*(max(len1,len2)/(min(len1,len2) + 1e-9));
return bitScore;
}/*}}}*/
void PrintKMerVectorPair_table(int* freqTable1, int* freqTable2, vector<int>& indexWordHit1, vector <int> & indexWordHit2, string& id1, string& id2, FILE *fpout) {/*{{{*/
set <int> unionKeys;
unionKeys.insert(indexWordHit1.begin(),indexWordHit1.end());
unionKeys.insert(indexWordHit2.begin(),indexWordHit2.end());
set <int> ::iterator it;
fprintf(fpout, "\n%13s%10s%13s %d (%d - %d)\n", id1.c_str(), "", id2.c_str(), (int)unionKeys.size(), (int)indexWordHit1.size(), (int)indexWordHit2.size());
}/*}}}*/
int CountKMerOfSequence_table(const char*seq, int len, int* freqTable, set <int>&indexWordHit, int wordsize){/*{{{*/
set <int> ::iterator it;
for (int i= 0; i < len - wordsize + 1 ; i++){
int idx = 0;
for (int j = 0; j < wordsize; j++){
idx += *(aacode+seq[i+j]) * para20[wordsize-j-1];
}
it = indexWordHit.find(idx);
if (it == indexWordHit.end()){
indexWordHit.insert(idx);
freqTable[idx] = 1;
}else{
freqTable[idx] ++;
}
}
return indexWordHit.size();
}/*}}}*/
int CountKMerOfSequence_table_2(const char*seq, int len, int *freqTable, vector <int>&indexWordHit, int wordsize){/*{{{*/
int numTotalWord = len-wordsize +1; /*number of words with duplicates*/
int *idxList = new int [numTotalWord];
for (int i= 0; i < numTotalWord ; i++){
int idx = 0;
for (int j = 0; j < wordsize; j++){
idx += *(aacode+seq[i+j]) * para20[wordsize-j-1];
}
idxList[i] = idx;
freqTable[idx] = 0;
}
for (int i= 0; i < numTotalWord ; i++){
freqTable[idxList[i]] ++;
}
vector <int> newlist(idxList, idxList+numTotalWord);
vector <int> :: iterator it;
sort (newlist.begin(),newlist.end());
it = unique(newlist.begin(),newlist.end());
newlist.resize(it - newlist.begin());/*this must be added to actually get a uniq list*/
indexWordHit = newlist;
//indexWordHit.insert(idxList, idxList+numTotalWord); [>this takes 90% of time for this function<]
delete [] idxList;
return indexWordHit.size();
}/*}}}*/
float CalKMerVectorScore_norm_table(int * freqTable1, int* freqTable2, set <int> indexWordHit1, set <int> indexWordHit2){/*{{{*/
float bitScore = 0.0;
float numWord1 = (float)indexWordHit1.size();
float numWord2 = (float)indexWordHit2.size();
set <int> index_intersection;
set <int> index_1_minus_2;
set <int> index_2_minus_1;
set_intersection(indexWordHit1.begin(), indexWordHit1.end(),
indexWordHit2.begin(),indexWordHit2.end(),
inserter(index_intersection,index_intersection.begin()));
set_difference(indexWordHit1.begin(), indexWordHit1.end(),
indexWordHit2.begin(),indexWordHit2.end(),
inserter(index_1_minus_2, index_1_minus_2.begin()));
set_difference(indexWordHit2.begin(), indexWordHit2.end(),
indexWordHit1.begin(),indexWordHit1.end(),
inserter(index_2_minus_1, index_2_minus_1.begin()));
set <int> ::iterator it;
for (it = index_intersection.begin(); it != index_intersection.end(); it++){
bitScore -= fabs(freqTable1[*it]/numWord1 - freqTable2[*it]/numWord2);
}
for (it = index_1_minus_2.begin(); it != index_1_minus_2.end(); it++){
bitScore -= fabs(freqTable1[*it]/numWord1);
}
for (it = index_2_minus_1.begin(); it != index_2_minus_1.end(); it++){
bitScore -= fabs(freqTable2[*it]/numWord2);
}
return bitScore;
}/*}}}*/
float CalKMerVectorScore_norm_table_2(int * freqTable1, int* freqTable2, vector <int> indexWordHit1, vector <int> indexWordHit2){/*{{{*/
float bitScore = 0.0;
float numWord1 = (float)indexWordHit1.size();
float numWord2 = (float)indexWordHit2.size();
vector <int> index_intersection;
vector <int> index_1_minus_2;
vector <int> index_2_minus_1;
set_intersection(indexWordHit1.begin(), indexWordHit1.end(),
indexWordHit2.begin(),indexWordHit2.end(),
inserter(index_intersection,index_intersection.begin()));
set_difference(indexWordHit1.begin(), indexWordHit1.end(),
indexWordHit2.begin(),indexWordHit2.end(),
inserter(index_1_minus_2, index_1_minus_2.begin()));
set_difference(indexWordHit2.begin(), indexWordHit2.end(),
indexWordHit1.begin(),indexWordHit1.end(),
inserter(index_2_minus_1, index_2_minus_1.begin()));
#ifdef DEBUG_SET_OPT/*{{{*/
fprintf(stdout,"vector1(%d):\n", int(numWord1));
for (int i = 0; i < int(numWord1); i++){
fprintf(stdout,"%3d ", indexWordHit1[i]);
}
fprintf(stdout,"\n");
fprintf(stdout,"vector2(%d):\n", int(numWord2));
for (int i = 0; i < int(numWord2); i++){
fprintf(stdout,"%3d ", indexWordHit2[i]);
}
fprintf(stdout,"\n");
fprintf(stdout,"vector intersection(%d):\n", int(index_intersection.size()));
for (int i = 0; i < index_intersection.size(); i++){
fprintf(stdout,"%3d ", (index_intersection.begin())[i]);
}
fprintf(stdout,"\n");
fprintf(stdout,"vector diff 1(%d):\n", int(index_1_minus_2.size()));
for (int i = 0; i < index_1_minus_2.size(); i++){
fprintf(stdout,"%3d ", (index_1_minus_2.begin())[i]);
}
fprintf(stdout,"\n");
#endif /*}}}*/
vector <int> ::iterator it;
for (it = index_intersection.begin(); it != index_intersection.end(); it++){
bitScore -= fabs(freqTable1[*it]/numWord1 - freqTable2[*it]/numWord2);
}
for (it = index_1_minus_2.begin(); it != index_1_minus_2.end(); it++){
bitScore -= (freqTable1[*it]/numWord1);
}
for (it = index_2_minus_1.begin(); it != index_2_minus_1.end(); it++){
bitScore -= (freqTable2[*it]/numWord2);
}
return bitScore;
}/*}}}*/
float KMerVectorPairwiseComparison_table(string& seq1, string& seq2, string& seqID1, string& seqID2, int* freqTable1, int *freqTable2, int sizeTable, int wordsize, FILE *fpLog){/*{{{*/
/*keep a table*/
int len1 = seq1.size();
int len2 = seq2.size();
vector <int> indexWordHit1;
vector <int> indexWordHit2;
CountKMerOfSequence_table_2(seq1.c_str(), len1, freqTable1, indexWordHit1, wordsize);
CountKMerOfSequence_table_2(seq2.c_str(), len2, freqTable2, indexWordHit2, wordsize);
#ifdef DEBUG_KMER
PrintKMerVectorPair_table(freqTable1,freqTable2, indexWordHit1,indexWordHit2, seqID1, seqID2, stdout);
#endif
//return 0.0;
float bitScore ;
//float bitScore = CalKMerVectorScore_norm_table(freqTable1, freqTable2, indexWordHit1, indexWordHit2);
bitScore = CalKMerVectorScore_norm_table_2(freqTable1, freqTable2, indexWordHit1, indexWordHit2);
//bitScore = bitScore*(max(len1,len2))/1000;
return bitScore;
}/*}}}*/
int ReadInPairList(const char* file, vector <Pair>&pairList)/*{{{*/
{
ifstream ifp (file, ios::binary);
if (ifp.is_open()){
ifp.seekg (0, ios::end);
int length = ifp.tellg();
ifp.seekg (0, ios::beg);
char *buffer = new char [ length+1];
ifp.read(buffer,length);
ifp.close();
buffer[length] = '\0';
char *pch;
pch = strtok(buffer, "\n");
Pair tmppair;