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diff mafft/core/pair2hat3s.c @ 18:e4d75f9efb90 draft

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planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
author nick
date Thu, 02 Feb 2017 18:44:31 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mafft/core/pair2hat3s.c	Thu Feb 02 18:44:31 2017 -0500
@@ -0,0 +1,468 @@
+#include "mltaln.h"
+
+#define DEBUG 0
+#define IODEBUG 0
+#define SCOREOUT 1
+#define TSUYOSAFACTOR 100
+
+
+static char *pairfile;
+static int nhomologs;
+
+void strip( char *s )
+{
+	char *pt = s;
+	while( *++pt )
+		if( *pt == '\n' ) *pt = 0;
+}
+
+int searchused( char *q, char **keys, int n )
+{
+	int i;
+	for( i=0; i<n; i++ )
+	{
+//		fprintf( stderr, "%s ? %s\n", q, names[i] );
+		if( !strcmp( q, keys[i] ) ) return( i );
+	}
+	return( -1 );
+}
+
+void arguments( int argc, char *argv[] )
+{
+    int c;
+
+	nhomologs = 2;
+	inputfile = NULL;
+	pairfile = NULL;
+	fftkeika = 0;
+	pslocal = -1000.0;
+	constraint = 0;
+	nblosum = 62;
+	fmodel = 0;
+	calledByXced = 0;
+	devide = 0;
+	use_fft = 0;
+	fftscore = 1;
+	fftRepeatStop = 0;
+	fftNoAnchStop = 0;
+    weight = 3;
+    utree = 1;
+	tbutree = 1;
+    refine = 0;
+    check = 1;
+    cut = 0.0;
+    disp = 0;
+    outgap = 1;
+    alg = 'A';
+    mix = 0;
+	tbitr = 0;
+	scmtd = 5;
+	tbweight = 0;
+	tbrweight = 3;
+	checkC = 0;
+	treemethod = 'x';
+	contin = 0;
+	scoremtx = 1;
+	kobetsubunkatsu = 0;
+	divpairscore = 0;
+	dorp = NOTSPECIFIED;
+	ppenalty = NOTSPECIFIED;
+	ppenalty_OP = NOTSPECIFIED;
+	ppenalty_ex = NOTSPECIFIED;
+	ppenalty_EX = NOTSPECIFIED;
+	poffset = NOTSPECIFIED;
+	kimuraR = NOTSPECIFIED;
+	pamN = NOTSPECIFIED;
+	geta2 = GETA2;
+	fftWinSize = NOTSPECIFIED;
+	fftThreshold = NOTSPECIFIED;
+
+    while( --argc > 0 && (*++argv)[0] == '-' )
+	{
+        while ( ( c = *++argv[0] ) )
+		{
+            switch( c )
+            {
+				case 'i':
+					inputfile = *++argv;
+					fprintf( stderr, "inputfile = %s\n", inputfile );
+					--argc;
+					goto nextoption;
+				case 'p':
+					pairfile = *++argv;
+					fprintf( stderr, "pairfile = %s\n", pairfile );
+					--argc;
+					goto nextoption;
+				case 't':
+					nhomologs = myatoi( *++argv );
+					fprintf( stderr, "nhomologs = %d\n", nhomologs );
+					--argc;
+					goto nextoption;
+				case 'D':
+					dorp = 'd';
+					break;
+				case 'P':
+					dorp = 'p';
+					break;
+                default:
+                    fprintf( stderr, "illegal option %c\n", c );
+                    argc = 0;
+                    break;
+            }
+		}
+		nextoption:
+			;
+	}
+    if( argc == 1 )
+    {
+        cut = atof( (*argv) );
+        argc--;
+    }
+    if( argc != 0 ) 
+    {
+        fprintf( stderr, "options: Check source file !\n" );
+        exit( 1 );
+    }
+	if( tbitr == 1 && outgap == 0 )
+	{
+		fprintf( stderr, "conflicting options : o, m or u\n" );
+		exit( 1 );
+	}
+	if( alg == 'C' && outgap == 0 )
+	{
+		fprintf( stderr, "conflicting options : C, o\n" );
+		exit( 1 );
+	}
+}
+
+int countamino( char *s, int end )
+{
+	int val = 0;
+	while( end-- )
+		if( *s++ != '-' ) val++;
+	return( val );
+}
+
+static void pairalign( char **name, int nlen[M], char **seq, double *effarr, int alloclen )
+{
+	FILE *tmpfp;
+	static char dumm1[B], dumm0[B];
+	int i, j;
+	char *res;
+	FILE *hat3p;
+	static double *effarr1 = NULL;
+	static double *effarr2 = NULL;
+	static char **pseq;
+	LocalHom **localhomtable, *tmpptr;
+	float pscore = 0.0; // by D.Mathog, aguess
+	char *aseq = NULL; // by D.Mathog
+	char **usedseqs = NULL; // by D.Mathog
+	char **usednames = NULL; // by D.Mathog
+	int nused;
+	double tsuyosa;
+
+	tsuyosa = (double)nhomologs * (nhomologs-1) / njob * TSUYOSAFACTOR;
+	fprintf( stderr, "tsuyosa = %f\n", tsuyosa );
+	localhomtable = (LocalHom **)calloc( njob, sizeof( LocalHom *) );
+	for( i=0; i<njob; i++)
+	{
+		localhomtable[i] = (LocalHom *)calloc( njob, sizeof( LocalHom ) );
+		for( j=0; j<njob; j++)
+		{
+			localhomtable[i][j].start1 = -1;
+			localhomtable[i][j].end1 = -1;
+			localhomtable[i][j].start2 = -1; 
+			localhomtable[i][j].end2 = -1; 
+			localhomtable[i][j].opt = -1.0;
+			localhomtable[i][j].next = NULL;
+		}
+	}
+
+	if( effarr1 == NULL ) 
+	{
+		effarr1 = AllocateDoubleVec( njob );
+		effarr2 = AllocateDoubleVec( njob );
+		pseq = AllocateCharMtx( 2, nlenmax*9+1 );
+		aseq = AllocateCharVec( nlenmax*9+1 );
+		usedseqs = AllocateCharMtx( njob, nlenmax*9+1 );
+		usednames = AllocateCharMtx( njob, B );
+#if 0
+#else
+#endif
+	}
+
+#if 0
+	fprintf( stderr, "##### fftwinsize = %d, fftthreshold = %d\n", fftWinSize, fftThreshold );
+#endif
+
+#if 0
+	for( i=0; i<njob; i++ )
+		fprintf( stderr, "TBFAST effarr[%d] = %f\n", i, effarr[i] );
+#endif
+
+
+//	writePre( njob, name, nlen, aseq, 0 );
+
+	fprintf( stderr, "opening %s\n", pairfile  );
+	tmpfp = fopen( pairfile, "r" );
+	if( !tmpfp )
+	{
+		fprintf( stderr, "Cannot open %s\n", pairfile );
+		exit( 1 );
+	}
+	searchKUorWA( tmpfp );
+	hat3p = fopen( "hat3", "w" );
+	if( !hat3p ) ErrorExit( "Cannot open hat3." );
+	nused = 0;
+	while( 1 )
+	{
+		res = fgets( dumm0, B-1, tmpfp );
+		strip( dumm0 );
+		if( res == NULL )
+		{
+			break;
+		}
+		load1SeqWithoutName_new( tmpfp, pseq[0] );
+		gappick0( aseq, pseq[0] );
+		i =  searchused( aseq, usedseqs, nused );
+		if( i == -1 )
+		{
+			strcpy( usednames[nused], dumm0+1 );
+			strcpy( usedseqs[nused], aseq );
+			i = nused;
+			nused++;
+		}
+		fprintf( stderr, "i = %d\n", i );
+
+		res = fgets( dumm1, B-1, tmpfp );
+		strip( dumm1 );
+		if( res == NULL )
+		{
+			fprintf( stderr, "ERROR: The number of sequences in %s must be even.\n", pairfile );
+			exit( 1 );
+		}
+		load1SeqWithoutName_new( tmpfp, pseq[1] );
+		gappick0( aseq, pseq[1] );
+		j =  searchused( aseq, usedseqs, nused );
+		if( j == -1 )
+		{
+			strcpy( usednames[nused], dumm1+1 );
+			strcpy( usedseqs[nused], aseq );
+			j = nused;
+			nused++;
+		}
+		fprintf( stderr, "j = %d\n", j );
+
+		if( strlen( pseq[0] ) != strlen( pseq[1] ) )
+		{
+			fprintf( stderr, "Not aligned,  %s - %s\n", dumm0, dumm1 );
+			exit( 1 );
+		}
+
+
+		fprintf( stderr, "adding %d-%d\n", i, j );
+		putlocalhom2( pseq[0], pseq[1], localhomtable[i]+j, 0, 0, (int)pscore, strlen( pseq[0] ) );
+		for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next )
+		{
+			if( tmpptr->opt == -1.0 ) continue;
+			fprintf( hat3p, "%d %d %d %6.3f %d %d %d %d %p\n", i, j, tmpptr->overlapaa, tmpptr->opt * tsuyosa, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, (void *)tmpptr->next ); 
+		}
+	}
+	fclose( tmpfp );
+	fclose( hat3p );
+
+	for( i=0; i<nused; i++ )
+		fprintf( stdout, ">%s\n%s\n", usednames[i], usedseqs[i] );
+
+
+#if 0
+	fprintf( stderr, "##### writing hat3\n" );
+	hat3p = fopen( "hat3", "w" );
+	if( !hat3p ) ErrorExit( "Cannot open hat3." );
+	ilim = njob-1;	
+	for( i=0; i<ilim; i++ ) 
+	{
+		for( j=i+1; j<njob; j++ )
+		{
+			for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next )
+			{
+				if( tmpptr->opt == -1.0 ) continue;
+				fprintf( hat3p, "%d %d %d %6.3f %d %d %d %d %p\n", i, j, tmpptr->overlapaa, tmpptr->opt * tsuyosa, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->next ); 
+			}
+		}
+	}
+	fclose( hat3p );
+#endif
+#if DEBUG
+	fprintf( stderr, "calling FreeLocalHomTable\n" );
+#endif
+	FreeLocalHomTable( localhomtable, njob );
+#if DEBUG
+	fprintf( stderr, "done. FreeLocalHomTable\n" );
+#endif
+}
+
+static void WriteOptions( FILE *fp )
+{
+
+	if( dorp == 'd' ) fprintf( fp, "DNA\n" );
+	else
+	{
+		if     ( scoremtx ==  0 ) fprintf( fp, "JTT %dPAM\n", pamN );
+		else if( scoremtx ==  1 ) fprintf( fp, "BLOSUM %d\n", nblosum );
+		else if( scoremtx ==  2 ) fprintf( fp, "M-Y\n" );
+	}
+    fprintf( stderr, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
+    if( use_fft ) fprintf( fp, "FFT on\n" );
+
+	fprintf( fp, "tree-base method\n" );
+	if( tbrweight == 0 ) fprintf( fp, "unweighted\n" );
+	else if( tbrweight == 3 ) fprintf( fp, "clustalw-like weighting\n" );
+	if( tbitr || tbweight ) 
+	{
+		fprintf( fp, "iterate at each step\n" );
+		if( tbitr && tbrweight == 0 ) fprintf( fp, "  unweighted\n" ); 
+		if( tbitr && tbrweight == 3 ) fprintf( fp, "  reversely weighted\n" ); 
+		if( tbweight ) fprintf( fp, "  weighted\n" ); 
+		fprintf( fp, "\n" );
+	}
+
+   	 fprintf( fp, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
+
+	if( alg == 'a' )
+		fprintf( fp, "Algorithm A\n" );
+	else if( alg == 'A' ) 
+		fprintf( fp, "Algorithm A+\n" );
+	else if( alg == 'S' ) 
+		fprintf( fp, "Apgorithm S\n" );
+	else if( alg == 'C' ) 
+		fprintf( fp, "Apgorithm A+/C\n" );
+	else
+		fprintf( fp, "Unknown algorithm\n" );
+
+	if( treemethod == 'x' )
+		fprintf( fp, "Tree = UPGMA (3).\n" );
+	else if( treemethod == 's' )
+		fprintf( fp, "Tree = UPGMA (2).\n" );
+	else if( treemethod == 'p' )
+		fprintf( fp, "Tree = UPGMA (1).\n" );
+	else
+		fprintf( fp, "Unknown tree.\n" );
+
+    if( use_fft )
+    {
+        fprintf( fp, "FFT on\n" );
+        if( dorp == 'd' )
+            fprintf( fp, "Basis : 4 nucleotides\n" );
+        else
+        {
+            if( fftscore )
+                fprintf( fp, "Basis : Polarity and Volume\n" );
+            else
+                fprintf( fp, "Basis : 20 amino acids\n" );
+        }
+        fprintf( fp, "Threshold   of anchors = %d%%\n", fftThreshold );
+        fprintf( fp, "window size of anchors = %dsites\n", fftWinSize );
+    }
+	else
+        fprintf( fp, "FFT off\n" );
+	fflush( fp );
+}
+	 
+
+int main( int argc, char *argv[] )
+{
+	static int  nlen[M];	
+	static char **name, **seq;
+	static char **bseq;
+	static double *eff;
+	int i;
+	char c;
+	int alloclen;
+	FILE *infp;
+
+	arguments( argc, argv );
+
+	if( inputfile )
+	{
+		infp = fopen( inputfile, "r" );
+		if( !infp )
+		{
+			fprintf( stderr, "Cannot open %s\n", inputfile );
+			exit( 1 );
+		}
+	}
+	else
+		infp = stdin;
+
+	if( !pairfile )
+	{
+		fprintf( stderr, "Usage: %s -p pairfile -i inputfile \n", argv[0] );
+		exit( 1 );
+	}
+
+	getnumlen( infp );
+	rewind( infp );
+
+	if( njob < 2 )
+	{
+		fprintf( stderr, "At least 2 sequences should be input!\n"
+						 "Only %d sequence found.\n", njob ); 
+		exit( 1 );
+	}
+
+	name = AllocateCharMtx( njob, B+1 );
+	seq = AllocateCharMtx( njob, nlenmax*9+1 );
+	bseq = AllocateCharMtx( njob, nlenmax*9+1 );
+	alloclen = nlenmax*9;
+
+	eff = AllocateDoubleVec( njob );
+
+#if 0
+	Read( name, nlen, seq );
+#else
+	readData_pointer( infp, name, nlen, seq );
+#endif
+	fclose( infp );
+
+	constants( njob, seq );
+
+#if 0
+	fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );
+#endif
+
+	initSignalSM();
+
+	initFiles();
+
+	WriteOptions( trap_g );
+
+	c = seqcheck( seq );
+	if( c )
+	{
+		fprintf( stderr, "Illeagal character %c\n", c );
+		exit( 1 );
+	}
+
+//	writePre( njob, name, nlen, seq, 0 );
+
+	for( i=0; i<njob; i++ ) eff[i] = 1.0;
+
+
+	for( i=0; i<njob; i++ ) gappick0( bseq[i], seq[i] );
+
+
+	pairalign( name, nlen, bseq, eff, alloclen );
+
+	fprintf( trap_g, "done.\n" );
+#if DEBUG
+	fprintf( stderr, "closing trap_g\n" );
+#endif
+	fclose( trap_g );
+
+#if IODEBUG
+	fprintf( stderr, "OSHIMAI\n" );
+#endif
+	SHOWVERSION;
+	return( 0 );
+}