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pairash.c

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Last change on this file was 10371, checked in by aboeckma, 11 years ago
updated mafft version. Added extensions (no svn ignore, yet)
File size: 29.9 KB

Line
1	#include "mltaln.h"
2
3	#define DEBUG 0
4	#define IODEBUG 0
5	#define SCOREOUT 0
6
7	static int usecache;
8	static char *whereispairalign;
9	static char *odir;
10	static char *pdir;
11	static double scale;
12	static int *alreadyoutput;
13	static int equivthreshold;
14	static int equivwinsize;
15	static int equivshortestlen;
16
17	static void cutpath( char *s )
18	{
19	char *pos;
20	pos = s + strlen( s );
21
22	while( --pos >= s )
23	{
24	if( *pos == '/' ) break;
25	}
26
27	strcpy( s, pos+1 );
28	}
29
30	static char getchainid( char *s )
31	{
32	s += strlen( s ) - 2;
33	if( isspace( s[0] ) && isalnum( s[1] ) )
34	return( s[1] );
35	else
36	return( 'A' );
37	}
38
39	static void extractfirstword( char *s )
40	{
41	while( *s )
42	{
43	if( isspace( *s ) ) break;
44	s++;
45	}
46	*s = 0;
47	}
48
49	static char strip( char s )
50	{
51	char *v;
52
53	while( *s )
54	{
55	if( !isspace( *s ) ) break;
56	s++;
57	}
58	v = s;
59
60	s += strlen( v ) - 1;
61	while( s>=v )
62	{
63	if( !isspace( *s ) )
64	{
65	*(s+1) = 0;
66	break;
67	}
68	s--;
69	}
70
71	return( v );
72	}
73
74	#if 0
75	static void makeequivdouble( double d, char c )
76	{
77	while( *c )
78	{
79	d++ = (double)( c++ - '0' );
80	}
81	}
82
83	static void maskequiv( double *d, int n )
84	{
85	int halfwin;
86	int ok;
87	int i, j;
88
89	halfwin = (int)( equivwinsize / 2 );
90
91	for( i=0; i<n; i++ )
92	{
93	ok = 1;
94	for( j = i-halfwin; j<i+halfwin; j++ )
95	{
96	if( j<0 \|\| n=<j ) continue;
97	if( d[j] <= 0.0 )
98	{
99	ok = 0;
100	break;
101	}
102	}
103	if( ok == 0 ) d[i] = 0.0;
104	}
105	}
106	#else
107	static void maskequiv( double *d, int n )
108	{
109	int i, len;
110	int count;
111	len = 0;
112	double dbk, dori, *dbkori;
113
114	dbk = calloc( n, sizeof( double ) );
115
116	dbkori = dbk;
117	dori = d;
118	count = n;
119	while( count-- )
120	{
121	dbk++ = d++;
122	}
123
124	dbk = dbkori;
125	d = dori;
126	len = 0;
127
128
129	for( i=0; i<n; i++ )
130	{
131	if( d[i] > 0.0 )
132	{
133	len += 1;
134	d[i] = 0.0;
135	}
136	else
137	{
138	d[i] = 0.0;
139	if( len >= equivshortestlen )
140	{
141	len++;
142	while( len-- ) d[i-len] = dbk[i-len];
143	}
144	len = 0;
145	}
146	}
147
148	if( len >= equivshortestlen )
149	{
150	len++;
151	while( len-- ) d[n-len] = dbk[n-len];
152	}
153
154	free( dbk );
155	}
156	#endif
157
158	static void makeequivdouble_tmalign( double d, char c, int n )
159	{
160	double tmpd;
161	double *dbk;
162	int tmpi;
163	char s;
164	dbk = d;
165	while( *c )
166	{
167	if( ( s=*c++ ) == ':' )
168	tmpi = 9;
169	else if( s == '.' )
170	tmpi = 4;
171	else
172	tmpi = 0;
173	// tmpd = (double)( tmpi + 1 - equivthreshold ) / ( 10 - equivthreshold ) * 9.0;
174	// if( tmpd < 0.0 ) tmpd = 0.0;
175	tmpd = (double)( tmpi );
176	// *d++ = (int)tmpd;
177	*d++ = tmpd;
178	}
179
180	d = dbk;
181	// maskequiv( d, n );
182	}
183
184	static void makeequivdouble_threshold( double d, char c, int n )
185	{
186	double tmpd;
187	double *dbk;
188	int tmpi;
189	dbk = d;
190	while( *c )
191	{
192	tmpi = (int)( *c++ - '0' );
193	tmpd = (double)( tmpi + 1 - equivthreshold ) / ( 10 - equivthreshold ) * 9.0;
194	if( tmpd < 0.0 ) tmpd = 0.0;
195	// *d++ = (int)tmpd;
196	*d++ = tmpd;
197	}
198
199	d = dbk;
200	maskequiv( d, n );
201	}
202
203	static void readtmalign( FILE fp, char seq1, char seq2, double equiv )
204	{
205	static char *line = NULL;
206	static char *equivchar = NULL;
207	int n;
208
209
210	if( equivchar == NULL )
211	{
212	equivchar = calloc( nlenmax * 2 + 1, sizeof( char ) );
213	line = calloc( nlenmax * 2 + 1, sizeof( char ) );
214	}
215	seq1[0] = 0;
216	seq2[0] = 0;
217	equivchar[0] = 0;
218
219
220	// system( "vi _tmalignout" );
221	while( 1 )
222	{
223	if( feof( fp ) )
224	{
225	fprintf( stderr, "Error in TMalign\n" );
226	exit( 1 );
227	}
228	fgets( line, 999, fp );
229	// fprintf( stdout, "line = :%s:\n", line );
230	if( !strncmp( line+5, "denotes the residue pairs", 20 ) ) break;
231	}
232	fgets( line, nlenmax*2, fp );
233	strcat( seq1, strip( line ) );
234
235	fgets( line, nlenmax*2, fp );
236	strcat( equivchar, strip( line ) );
237
238	fgets( line, nlenmax*2, fp );
239	strcat( seq2, strip( line ) );
240
241	#if 0
242	printf( "seq1=%s\n", seq1 );
243	printf( "seq2=%s\n", seq2 );
244	printf( "equi=%s\n", equivchar );
245	exit( 1 );
246	#endif
247	n = strlen( seq1 );
248	makeequivdouble_tmalign( equiv, equivchar, n );
249
250	#if 0
251	fprintf( stdout, "\n" );
252	for( i=0; i<n; i++ )
253	{
254	fprintf( stdout, "%1.0f", equiv[i] );
255	}
256	fprintf( stdout, "\n" );
257	exit( 1 );
258	#endif
259	}
260	static void readrash( FILE fp, char seq1, char seq2, double equiv )
261	{
262	char line[1000];
263	static char *equivchar = NULL;
264	int n;
265
266
267	if( equivchar == NULL )
268	{
269	equivchar = calloc( nlenmax * 2, sizeof( char ) );
270	}
271	seq1[0] = 0;
272	seq2[0] = 0;
273	equivchar[0] = 0;
274
275	while( 1 )
276	{
277	fgets( line, 999, fp );
278	// fprintf( stdout, "line = :%s:\n", line );
279	if( !strncmp( line, "Query ", 6 ) ) break;
280	if( feof( fp ) ) break;
281	if( !strncmp( line, "QUERY ", 6 ) )
282	{
283	strcat( seq1, strip( line+5 ) );
284	fgets( line, 999, fp );
285	}
286	if( !strncmp( line, "TEMPL ", 6 ) )
287	{
288	strcat( seq2, strip( line+5 ) );
289	fgets( line, 999, fp );
290	}
291	if( !strncmp( line, "Equiva", 6 ) )
292	{
293	strcat( equivchar, strip( line+11 ) );
294	fgets( line, 999, fp );
295	}
296	}
297	#if 0
298	printf( "seq1=:%s:\n", seq1 );
299	printf( "seq2=:%s:\n", seq2 );
300	printf( "equi=:%s:\n", equivchar );
301	exit( 1 );
302	#endif
303	n = strlen( seq1 );
304	makeequivdouble_threshold( equiv, equivchar, n );
305
306	#if 0
307	fprintf( stdout, "\n" );
308	for( i=0; i<n; i++ )
309	{
310	fprintf( stdout, "%1.0f", equiv[i] );
311	}
312	fprintf( stdout, "\n" );
313	#endif
314	}
315
316	static int checkcbeta( FILE *fp )
317	{
318	char linec[1000];
319	while( 1 )
320	{
321	fgets( linec, 999, fp );
322	if( feof( fp ) ) break;
323	if( !strncmp( "ATOM ", linec, 5 ) )
324	{
325	if( !strncmp( "CB ", linec+13, 3 ) ) return( 0 );
326	}
327	}
328	return( 1 );
329	}
330
331
332	static float calltmalign( char mseq1, char mseq2, double equiv, char fname1, char chain1, char fname2, char *chain2, int alloclen )
333	{
334	FILE *fp;
335	int res;
336	static char com[10000];
337	float value;
338	char cachedir[10000];
339	char cachefile[10000];
340	int runnow;
341
342
343	if( usecache )
344	{
345	sprintf( cachedir, "%s/.tmalignoutcache", getenv( "HOME" ) );
346	sprintf( com, "mkdir -p %s", cachedir );
347	system( com );
348
349	sprintf( cachefile, "%s/%s%s-%s%s", cachedir, fname1, chain1, fname2, chain2 );
350
351	runnow = 0;
352	fp = fopen( cachefile, "r" );
353	if( fp == NULL ) runnow = 1;
354	else
355	{
356	fgets( com, 100, fp );
357	if( strncmp( com, "successful", 10 ) ) runnow = 1;
358	fclose( fp );
359	}
360	}
361	else
362	{
363	runnow = 1;
364	}
365
366	if( runnow )
367	{
368	#if 0
369	sprintf( com, "ln -s %s %s.pdb 2>_dum", fname1, fname1 );
370	res = system( com );
371	sprintf( com, "ln -s %s %s.pdb 2>_dum", fname2, fname2 );
372	res = system( com );
373	#endif
374	sprintf( com, "\"%s/TMalign\" %s.pdb %s.pdb > _tmalignout 2>_dum", whereispairalign, fname1, fname2 );
375	fprintf( stderr, "command = %s\n", com );
376	res = system( com );
377	if( res )
378	{
379	fprintf( stderr, "Error in TMalign\n" );
380	exit( 1 );
381	}
382
383	}
384	else
385	{
386	fprintf( stderr, "Cache is not supported!\n" );
387	exit( 1 );
388	}
389
390	fp = fopen( "_tmalignout", "r" );
391	if( !fp )
392	{
393	fprintf( stderr, "Cannot open _tmalignout\n" );
394	exit( 1 );
395	}
396
397	readtmalign( fp, mseq1, mseq2, equiv );
398
399	fclose( fp );
400
401	// fprintf( stderr, "mseq1 = %s\n", mseq1 );
402	// fprintf( stderr, "mseq2 = %s\n", mseq2 );
403
404	value = (float)naivepairscore11( mseq1, mseq2, penalty );
405
406	return( value );
407	}
408
409	static float callrash( int mem1, int mem2, char mseq1, char mseq2, double equiv, char fname1, char *fname2, int alloclen )
410	{
411	FILE *fp;
412	// int res;
413	static char com[10000];
414	float value;
415	char cachedir[10000];
416	char cachefile[10000];
417	int runnow;
418	char pairid[1000];
419
420	sprintf( pairid, "%d-%d", mem1, mem2 );
421	// fprintf( stderr, "pairid = %s\n", pairid );
422
423	if( usecache )
424	{
425	// sprintf( cachedir, "tmp" );
426	sprintf( cachedir, "%s", pdir );
427
428	sprintf( cachefile, "%s/%s.%s.rash", cachedir, fname1, fname2 );
429
430	runnow = 0;
431	fp = fopen( cachefile, "r" );
432	if( fp == NULL )
433	{
434	fprintf( stderr, "Cannot open %s\n", cachefile );
435	exit( 1 );
436	}
437	else
438	{
439	fclose( fp );
440	}
441	}
442	else
443	{
444	fprintf( stderr, "Not supported!\n" );
445	exit( 1 );
446	}
447
448	#if 0
449	if( 0 )
450	{
451	#if 0
452	sprintf( com, "ln -s %s %s.pdb 2>_dum", fname1, fname1 );
453	res = system( com );
454	sprintf( com, "ln -s %s %s.pdb 2>_dum", fname2, fname2 );
455	res = system( com );
456	#endif
457	#if 0 // 091127, pdp nai!
458	sprintf( com, "env PATH=%s PDP_ASH.pl --qf %s.pdb --qc %s --tf %s.pdb --tc %s > _rashout 2>_dum", whereispairalign, fname1, chain1, fname2, chain2 );
459	#else
460	sprintf( com, "\"%s/rash\" --qf %s.pdb --qc %s --tf %s.pdb --tc %s --of %s.pdbpair > %s.rashout 2>%s.dum", whereispairalign, fname1, chain1, fname2, chain2, pairid, pairid, pairid );
461	#endif
462	fprintf( stderr, "command = %s\n", com );
463	res = system( com );
464	if( res )
465	{
466	fprintf( stderr, "Error in structural alignment\n" );
467	exit( 1 );
468	}
469	sprintf( com, "awk '/^REMARK/,/^TER/' %s.pdbpair > %s.%s-x-%s.%s.pdbpair", pairid, fname1, chain1, fname2, chain2 );
470	res = system( com );
471
472	sprintf( com, "awk '/^REMARK/,/^TER/{next} 1' %s.pdbpair > %s.%s-x-%s.%s.pdbpair", pairid, fname2, chain2, fname1, chain1 );
473	res = system( com );
474
475	sprintf( com, "rm %s.pdbpair", pairid );
476	res = system( com );
477
478
479	}
480	else
481	#endif
482	{
483	fprintf( stderr, "Use cache! cachefile = %s\n", cachefile );
484	sprintf( com, "cat %s > %s.rashout", cachefile, pairid );
485	system( com );
486	}
487
488	if( usecache && runnow )
489	{
490	fprintf( stderr, "Okashii! usechache=%d, runnow=%d\n", usecache, runnow );
491	exit( 1 );
492	}
493
494	sprintf( com, "%s.rashout", pairid );
495	fp = fopen( com, "r" );
496	if( !fp )
497	{
498	fprintf( stderr, "Cannot open %s\n", com );
499	exit( 1 );
500	}
501
502	readrash( fp, mseq1, mseq2, equiv );
503
504	fclose( fp );
505
506	// fprintf( stderr, "mseq1 = %s\n", mseq1 );
507	// fprintf( stderr, "mseq2 = %s\n", mseq2 );
508
509
510	value = (float)naivepairscore11( mseq1, mseq2, penalty );
511
512	return( value );
513	}
514
515	static void preparetmalign( FILE fp, char strfiles, char chainids, char seqpt, char mseq1pt, char mseq2pt, double equivpt, int *alloclenpt )
516	{
517	int i, res;
518	char *dumseq;
519	char line[1000];
520	char fname[1000];
521	char command[1000];
522	int linenum, istr, nstr;
523	FILE *checkfp;
524	char *sline;
525	int use[1000];
526	linenum = 0;
527	nstr = 0;
528	while( 1 )
529	{
530	fgets( line, 999, fp );
531	if( feof( fp ) ) break;
532	sline = strip( line );
533	use[linenum] = 1;
534	if( sline[0] == '#' \|\| strlen( sline ) < 2 )
535	{
536	use[linenum] = 0;
537	linenum++;
538	continue;
539	}
540	extractfirstword( sline );
541	checkfp = fopen( sline, "r" );
542	if( checkfp == NULL )
543	{
544	fprintf( stderr, "Cannot open %s.\n", sline );
545	exit( 1 );
546	}
547	#if 0
548	fgets( linec, 999, checkfp );
549	if( strncmp( "HEADER ", linec, 7 ) )
550	{
551	fprintf( stderr, "Check the format of %s.\n", sline );
552	exit( 1 );
553	}
554	#endif
555	if( checkcbeta( checkfp ) )
556	{
557	fprintf( stderr, "%s has no C-beta atoms.\n", sline );
558	exit( 1 );
559	}
560	else
561	nstr++;
562	fclose( checkfp );
563	linenum++;
564	}
565	njob = nstr;
566	fprintf( stderr, "nstr = %d\n", nstr );
567
568	*strfiles = AllocateCharMtx( nstr, 1000 );
569	*chainids = AllocateCharMtx( nstr, 2 );
570
571	rewind( fp );
572	istr = 0;
573	linenum = 0;
574	while( 1 )
575	{
576	fgets( line, 999, fp );
577	if( feof( fp ) ) break;
578	sline = strip( line );
579	if( use[linenum++] )
580	{
581	(*chainids)[istr][0] = getchainid( sline );
582	(*chainids)[istr][1] = 0;
583	extractfirstword( sline );
584	sprintf( fname, "%s", sline );
585	cutpath( fname );
586	sprintf( command, "cp %s %s.pdb", sline, fname );
587	system( command );
588	sprintf( command, "perl \"%s/clean.pl\" %s.pdb", whereispairalign, fname );
589	res = system( command );
590	if( res )
591	{
592	fprintf( stderr, "error: Install clean.pl\n" );
593	exit( 1 );
594	}
595	strcpy( (*strfiles)[istr++], fname );
596	}
597	}
598
599	seqpt = AllocateCharMtx( njob, nlenmax2+1 );
600	*mseq1pt = AllocateCharMtx( njob, 0 );
601	*mseq2pt = AllocateCharMtx( njob, 0 );
602	equivpt = AllocateDoubleVec( nlenmax2+1 );
603	alloclenpt = nlenmax2;
604	dumseq = AllocateCharVec( nlenmax*2+1 );
605	alreadyoutput = AllocateIntVec( njob );
606	for( i=0; i<njob; i++ ) alreadyoutput[i] = 0;
607
608	for( i=0; i<istr; i++ )
609	{
610	fprintf( stderr, "i=%d\n", i );
611	(*seqpt)[i][0] = 0;
612
613	(mseq1pt)[0] = (seqpt)[i];
614	(*mseq2pt)[0] = dumseq;
615
616	calltmalign( mseq1pt, mseq2pt, equivpt, (strfiles)[i], (chainids)[i], (strfiles)[i], (chainids)[i], alloclenpt );
617	fprintf( stdout, ">%d_%s-%s\n%s\n", i+1, (strfiles)[i], (chainids)[i], (*seqpt)[i] );
618	alreadyoutput[i] = 1;
619	}
620	}
621
622	static void prepareash( FILE fp, char inputfile, char *strfiles, char chainids, char seqpt, char mseq1pt, char mseq2pt, double equivpt, int *alloclenpt )
623	{
624	int i, res;
625	char *dumseq;
626	char line[1000];
627	char fname[1000];
628	char command[1000];
629	int linenum, istr, nstr;
630	// FILE *checkfp;
631	char *sline;
632	int use[1000];
633	linenum = 0;
634	nstr = 0;
635
636	fprintf( stderr, "inputfile = %s\n", inputfile );
637	while( 1 )
638	{
639	fgets( line, 999, fp );
640	if( feof( fp ) ) break;
641	sline = strip( line );
642	use[linenum] = 1;
643	if( sline[0] == '#' \|\| strlen( sline ) < 2 )
644	{
645	use[linenum] = 0;
646	linenum++;
647	continue;
648	}
649	extractfirstword( sline );
650	#if 0
651	checkfp = fopen( sline, "r" );
652	if( checkfp == NULL )
653	{
654	fprintf( stderr, "Cannot open %s.\n", sline );
655	exit( 1 );
656	}
657	if( checkcbeta( checkfp ) )
658	{
659	fprintf( stderr, "%s has no C-beta atoms.\n", sline );
660	exit( 1 );
661	}
662	else
663	nstr++;
664	fclose( checkfp );
665	#else
666	nstr++;
667	#endif
668	linenum++;
669	}
670	njob = nstr;
671	fprintf( stderr, "nstr = %d\n", nstr );
672
673	*strfiles = AllocateCharMtx( nstr, 1000 );
674	*chainids = AllocateCharMtx( nstr, 2 );
675
676	rewind( fp );
677	istr = 0;
678	linenum = 0;
679	while( 1 )
680	{
681	fgets( line, 999, fp );
682	if( feof( fp ) ) break;
683	sline = strip( line );
684	fprintf( stderr, "sline = %s\n", sline );
685	if( use[linenum++] )
686	{
687	(*chainids)[istr][0] = getchainid( sline );
688	(*chainids)[istr][1] = 0;
689	extractfirstword( sline );
690	sprintf( fname, "%s", sline );
691	cutpath( fname );
692	#if 0
693	sprintf( command, "cp %s %s.pdb", sline, fname );
694	system( command );
695	sprintf( command, "perl \"%s/clean.pl\" %s.pdb", whereispairalign, fname );
696	res = system( command );
697	if( res )
698	{
699	fprintf( stderr, "error: Install clean.pl\n" );
700	exit( 1 );
701	}
702	#endif
703	strcpy( (*strfiles)[istr++], fname );
704	}
705	}
706
707	seqpt = AllocateCharMtx( njob, nlenmax2+1 );
708	*mseq1pt = AllocateCharMtx( njob, 0 );
709	*mseq2pt = AllocateCharMtx( njob, 0 );
710	equivpt = AllocateDoubleVec( nlenmax2+1 );
711	alloclenpt = nlenmax2;
712	dumseq = AllocateCharVec( nlenmax*2+1 );
713	alreadyoutput = AllocateIntVec( njob );
714	for( i=0; i<njob; i++ ) alreadyoutput[i] = 0;
715
716	fprintf( stderr, "Running pdp_ash_batch.pl..\n" );
717	// sprintf( command, "/opt/protein/share/domains/code/pdp_ash/pdp_ash_batch.pl -f %s -d tmp -i %d", inputfile, wheretooutput );
718	sprintf( command, "/opt/protein/share/mafftash/pdp_ash/pdp_ash_batch.pl -f %s -d %s -i %s", inputfile, pdir, odir );
719	res = system( command );
720	if( res )
721	{
722	fprintf( stderr, "Ask KM!\n" );
723	exit( 1 );
724	}
725	fprintf( stderr, "done\n" );
726
727
728	for( i=0; i<istr; i++ )
729	{
730	fprintf( stderr, "i=%d\n", i );
731	(*seqpt)[i][0] = 0;
732
733	(mseq1pt)[0] = (seqpt)[i];
734	(*mseq2pt)[0] = dumseq;
735
736	callrash( i, i, mseq1pt, mseq2pt, equivpt, (strfiles)[i], (strfiles)[i], alloclenpt );
737	fprintf( stdout, ">%d_%s\n%s\n", i+1, (strfiles)[i], (seqpt)[i] );
738	alreadyoutput[i] = 1;
739	}
740	}
741
742	void arguments( int argc, char *argv[] )
743	{
744	int c;
745
746	usecache = 0;
747	scale = 1.0;
748	equivthreshold = 5;
749	equivwinsize = 5;
750	equivshortestlen = 1;
751	inputfile = NULL;
752	fftkeika = 0;
753	pslocal = -1000.0;
754	constraint = 0;
755	nblosum = 62;
756	fmodel = 0;
757	calledByXced = 0;
758	devide = 0;
759	use_fft = 0;
760	fftscore = 1;
761	fftRepeatStop = 0;
762	fftNoAnchStop = 0;
763	weight = 3;
764	utree = 1;
765	tbutree = 1;
766	refine = 0;
767	check = 1;
768	cut = 0.0;
769	disp = 0;
770	outgap = 1;
771	alg = 'R';
772	mix = 0;
773	tbitr = 0;
774	scmtd = 5;
775	tbweight = 0;
776	tbrweight = 3;
777	checkC = 0;
778	treemethod = 'x';
779	contin = 0;
780	scoremtx = 1;
781	kobetsubunkatsu = 0;
782	divpairscore = 0;
783	dorp = NOTSPECIFIED;
784	ppenalty = NOTSPECIFIED;
785	ppenalty_OP = NOTSPECIFIED;
786	ppenalty_ex = NOTSPECIFIED;
787	ppenalty_EX = NOTSPECIFIED;
788	poffset = NOTSPECIFIED;
789	kimuraR = NOTSPECIFIED;
790	pamN = NOTSPECIFIED;
791	geta2 = GETA2;
792	fftWinSize = NOTSPECIFIED;
793	fftThreshold = NOTSPECIFIED;
794	RNAppenalty = NOTSPECIFIED;
795	RNApthr = NOTSPECIFIED;
796	odir = "";
797	pdir = "";
798
799	while( --argc > 0 && (*++argv)[0] == '-' )
800	{
801	while ( ( c = *++argv[0] ) )
802	{
803	switch( c )
804	{
805	case 'i':
806	inputfile = *++argv;
807	fprintf( stderr, "inputfile = %s\n", inputfile );
808	--argc;
809	goto nextoption;
810	case 'f':
811	ppenalty = (int)( atof( ++argv ) 1000 - 0.5 );
812	--argc;
813	goto nextoption;
814	case 'g':
815	ppenalty_ex = (int)( atof( ++argv ) 1000 - 0.5 );
816	--argc;
817	goto nextoption;
818	case 'O':
819	ppenalty_OP = (int)( atof( ++argv ) 1000 - 0.5 );
820	--argc;
821	goto nextoption;
822	case 'E':
823	ppenalty_EX = (int)( atof( ++argv ) 1000 - 0.5 );
824	--argc;
825	goto nextoption;
826	case 'h':
827	poffset = (int)( atof( ++argv ) 1000 - 0.5 );
828	--argc;
829	goto nextoption;
830	case 'k':
831	kimuraR = atoi( *++argv );
832	// fprintf( stderr, "kimuraR = %d\n", kimuraR );
833	--argc;
834	goto nextoption;
835	case 'b':
836	nblosum = atoi( *++argv );
837	scoremtx = 1;
838	// fprintf( stderr, "blosum %d\n", nblosum );
839	--argc;
840	goto nextoption;
841	case 'j':
842	pamN = atoi( *++argv );
843	scoremtx = 0;
844	TMorJTT = JTT;
845	fprintf( stderr, "jtt %d\n", pamN );
846	--argc;
847	goto nextoption;
848	case 'm':
849	pamN = atoi( *++argv );
850	scoremtx = 0;
851	TMorJTT = TM;
852	fprintf( stderr, "TM %d\n", pamN );
853	--argc;
854	goto nextoption;
855	case 'd':
856	whereispairalign = *++argv;
857	fprintf( stderr, "whereispairalign = %s\n", whereispairalign );
858	--argc;
859	goto nextoption;
860	case 'o':
861	odir = *++argv;
862	fprintf( stderr, "odir = %s\n", odir );
863	--argc;
864	goto nextoption;
865	case 'p':
866	pdir = *++argv;
867	fprintf( stderr, "pdir = %s\n", pdir );
868	--argc;
869	goto nextoption;
870	case 't':
871	equivthreshold = atoi( *++argv );
872	--argc;
873	goto nextoption;
874	case 'w':
875	equivwinsize = atoi( *++argv );
876	--argc;
877	goto nextoption;
878	case 'l':
879	equivshortestlen = atoi( *++argv );
880	--argc;
881	goto nextoption;
882	case 's':
883	scale = atof( *++argv );
884	--argc;
885	goto nextoption;
886	case 'c':
887	usecache = 1;
888	break;
889	#if 1
890	case 'a':
891	fmodel = 1;
892	break;
893	#endif
894	case 'r':
895	fmodel = -1;
896	break;
897	case 'D':
898	dorp = 'd';
899	break;
900	case 'P':
901	dorp = 'p';
902	break;
903	case 'e':
904	fftscore = 0;
905	break;
906	#if 0
907	case 'O':
908	fftNoAnchStop = 1;
909	break;
910	#endif
911	case 'Q':
912	calledByXced = 1;
913	break;
914	case 'x':
915	disp = 1;
916	break;
917	#if 0
918	case 'a':
919	alg = 'a';
920	break;
921	#endif
922	case 'S':
923	alg = 'S';
924	break;
925	case 'L':
926	alg = 'L';
927	break;
928	case 'B':
929	alg = 'B';
930	break;
931	case 'T':
932	alg = 'T';
933	break;
934	case 'H':
935	alg = 'H';
936	break;
937	case 'M':
938	alg = 'M';
939	break;
940	case 'R':
941	alg = 'R';
942	break;
943	case 'N':
944	alg = 'N';
945	break;
946	case 'K':
947	alg = 'K';
948	break;
949	case 'A':
950	alg = 'A';
951	break;
952	case 'V':
953	alg = 'V';
954	break;
955	case 'C':
956	alg = 'C';
957	break;
958	case 'F':
959	use_fft = 1;
960	break;
961	case 'v':
962	tbrweight = 3;
963	break;
964	case 'y':
965	divpairscore = 1;
966	break;
967	/* Modified 01/08/27, default: user tree */
968	case 'J':
969	tbutree = 0;
970	break;
971	/* modification end. */
972	#if 0
973	case 'z':
974	fftThreshold = atoi( *++argv );
975	--argc;
976	goto nextoption;
977	case 'w':
978	fftWinSize = atoi( *++argv );
979	--argc;
980	goto nextoption;
981	case 'Z':
982	checkC = 1;
983	break;
984	#endif
985	default:
986	fprintf( stderr, "illegal option %c\n", c );
987	argc = 0;
988	break;
989	}
990	}
991	nextoption:
992	;
993	}
994	if( argc == 1 )
995	{
996	cut = atof( (*argv) );
997	argc--;
998	}
999	if( argc != 0 )
1000	{
1001	fprintf( stderr, "options: Check source file !\n" );
1002	exit( 1 );
1003	}
1004	if( tbitr == 1 && outgap == 0 )
1005	{
1006	fprintf( stderr, "conflicting options : o, m or u\n" );
1007	exit( 1 );
1008	}
1009	if( alg == 'C' && outgap == 0 )
1010	{
1011	fprintf( stderr, "conflicting options : C, o\n" );
1012	exit( 1 );
1013	}
1014	}
1015
1016	int countamino( char *s, int end )
1017	{
1018	int val = 0;
1019	while( end-- )
1020	if( *s++ != '-' ) val++;
1021	return( val );
1022	}
1023
1024	static void pairalign( char name, int nlen[M], char seq, char aseq, char mseq1, char *mseq2, double equiv, double effarr, char strfiles, char *chainids, int alloclen )
1025	{
1026	int i, j, ilim;
1027	int clus1, clus2;
1028	int off1, off2;
1029	float pscore = 0.0; // by D.Mathog
1030	static char indication1, indication2;
1031	FILE hat2p, hat3p;
1032	static double **distancemtx;
1033	static double *effarr1 = NULL;
1034	static double *effarr2 = NULL;
1035	char *pt;
1036	char *hat2file = "hat2";
1037	LocalHom *localhomtable, tmpptr;
1038	static char **pair;
1039	// int intdum;
1040	double bunbo;
1041	char **checkseq;
1042
1043
1044	localhomtable = (LocalHom *)calloc( njob, sizeof( LocalHom ) );
1045	for( i=0; i<njob; i++)
1046	{
1047
1048	localhomtable[i] = (LocalHom *)calloc( njob, sizeof( LocalHom ) );
1049	for( j=0; j<njob; j++)
1050	{
1051	localhomtable[i][j].start1 = -1;
1052	localhomtable[i][j].end1 = -1;
1053	localhomtable[i][j].start2 = -1;
1054	localhomtable[i][j].end2 = -1;
1055	localhomtable[i][j].opt = -1.0;
1056	localhomtable[i][j].next = NULL;
1057	localhomtable[i][j].nokori = 0;
1058	}
1059	}
1060
1061	if( effarr1 == NULL )
1062	{
1063	distancemtx = AllocateDoubleMtx( njob, njob );
1064	effarr1 = AllocateDoubleVec( njob );
1065	effarr2 = AllocateDoubleVec( njob );
1066	indication1 = AllocateCharVec( 150 );
1067	indication2 = AllocateCharVec( 150 );
1068	checkseq = AllocateCharMtx( njob, alloclen );
1069	#if 0
1070	#else
1071	pair = AllocateCharMtx( njob, njob );
1072	#endif
1073	}
1074
1075	#if 0
1076	fprintf( stderr, "##### fftwinsize = %d, fftthreshold = %d\n", fftWinSize, fftThreshold );
1077	#endif
1078
1079	#if 0
1080	for( i=0; i<njob; i++ )
1081	fprintf( stderr, "TBFAST effarr[%d] = %f\n", i, effarr[i] );
1082	#endif
1083
1084
1085	// writePre( njob, name, nlen, aseq, 0 );
1086
1087	for( i=0; i<njob; i++ ) for( j=0; j<njob; j++ ) pair[i][j] = 0;
1088	for( i=0; i<njob; i++ ) pair[i][i] = 1;
1089
1090	for( i=0; i<njob; i++ )
1091	{
1092	strcpy( checkseq[i], seq[i] );
1093	// fprintf( stderr, "checkseq[%d] = %s\n", i, checkseq[i] );
1094	}
1095
1096
1097	ilim = njob - 1;
1098	for( i=0; i<ilim; i++ )
1099	{
1100	fprintf( stderr, "% 5d / %d\r", i, njob );
1101
1102
1103	for( j=i+1; j<njob; j++ )
1104	{
1105
1106
1107	#if 0
1108	if( strlen( seq[i] ) == 0 \|\| strlen( seq[j] ) == 0 )
1109	{
1110	distancemtx[i][j] = pscore;
1111	continue;
1112	}
1113	#endif
1114
1115	strcpy( aseq[i], seq[i] );
1116	strcpy( aseq[j], seq[j] );
1117	clus1 = conjuctionfortbfast_old( pair, i, aseq, mseq1, effarr1, effarr, indication1 );
1118	clus2 = conjuctionfortbfast_old( pair, j, aseq, mseq2, effarr2, effarr, indication2 );
1119	// fprintf( stderr, "mseq1 = %s\n", mseq1[0] );
1120	// fprintf( stderr, "mseq2 = %s\n", mseq2[0] );
1121
1122	#if 0
1123	fprintf( stderr, "group1 = %.66s", indication1 );
1124	fprintf( stderr, "\n" );
1125	fprintf( stderr, "group2 = %.66s", indication2 );
1126	fprintf( stderr, "\n" );
1127	#endif
1128	// for( l=0; l<clus1; l++ ) fprintf( stderr, "## STEP-eff for mseq1-%d %f\n", l, effarr1[l] );
1129
1130	#if 1
1131	{
1132	switch( alg )
1133	{
1134	case( 'T' ):
1135	fprintf( stderr, " Calling tmalign %d-%d/%d \r", i+1, j+1, njob );
1136	pscore = calltmalign( mseq1, mseq2, equiv, strfiles[i], chainids[i], strfiles[j], chainids[j], alloclen );
1137	off1 = off2 = 0;
1138	break;
1139	case( 'R' ):
1140	fprintf( stderr, " Calling PDP_ASH.pl %d-%d/%d \r", i+1, j+1, njob );
1141	pscore = callrash( i, j, mseq1, mseq2, equiv, strfiles[i], strfiles[j], alloclen );
1142	off1 = off2 = 0;
1143	break;
1144	ErrorExit( "ERROR IN SOURCE FILE" );
1145	}
1146	}
1147	#endif
1148	distancemtx[i][j] = pscore;
1149	#if SCOREOUT
1150	fprintf( stderr, "score = %10.2f (%d,%d)\n", pscore, i, j );
1151	#endif
1152
1153	putlocalhom_str( mseq1[0], mseq2[0], equiv, scale, localhomtable[i]+j, off1, off2, (int)pscore, strlen( mseq1[0] ) );
1154	#if 1
1155
1156	if( alreadyoutput[i] == 0 )
1157	{
1158	alreadyoutput[i] = 1;
1159	gappick0( seq[i], mseq1[0] );
1160	fprintf( stdout, ">%d_%s\n%s\n", i+1, strfiles[i], seq[i] );
1161	strcpy( checkseq[i], seq[i] );
1162	}
1163	else
1164	{
1165	gappick0( seq[i], mseq1[0] );
1166	fprintf( stderr, "checking seq%d\n", i );
1167
1168	// fprintf( stderr, " seq=%s\n", seq[i] );
1169	// fprintf( stderr, "checkseq=%s\n", checkseq[i] );
1170
1171	if( strcmp( checkseq[i], seq[i] ) )
1172	{
1173	fprintf( stderr, "\n\nWARNING: Sequence changed!!\n" );
1174	fprintf( stderr, "i=%d\n", i );
1175	fprintf( stderr, " seq=%s\n", seq[i] );
1176	fprintf( stderr, "checkseq=%s\n", checkseq[i] );
1177	exit( 1 );
1178	}
1179	}
1180	if( alreadyoutput[j] == 0 )
1181	{
1182	alreadyoutput[j] = 1;
1183	gappick0( seq[j], mseq2[0] );
1184	fprintf( stdout, ">%d_%s-%s\n%s\n", j+1, strfiles[j], chainids[j], seq[j] );
1185	strcpy( checkseq[j], seq[j] );
1186	}
1187	else
1188	{
1189	gappick0( seq[j], mseq2[0] );
1190	fprintf( stderr, "checking seq%d\n", j );
1191	if( strcmp( checkseq[j], seq[j] ) )
1192	{
1193	fprintf( stderr, "\n\nWARNING: Sequence changed!!\n" );
1194	fprintf( stderr, "j=%d\n", j );
1195	fprintf( stderr, " seq=%s\n", seq[j] );
1196	fprintf( stderr, "checkseq=%s\n", checkseq[j] );
1197	exit( 1 );
1198	}
1199	}
1200	#endif
1201	}
1202	}
1203	for( i=0; i<njob; i++ )
1204	{
1205	pscore = 0.0;
1206	for( pt=seq[i]; *pt; pt++ )
1207	pscore += amino_dis[(int)pt][(int)pt];
1208	distancemtx[i][i] = pscore;
1209
1210	}
1211
1212	ilim = njob-1;
1213	for( i=0; i<ilim; i++ )
1214	{
1215	for( j=i+1; j<njob; j++ )
1216	{
1217	bunbo = MIN( distancemtx[i][i], distancemtx[j][j] );
1218	if( bunbo == 0.0 )
1219	distancemtx[i][j] = 2.0;
1220	else
1221	distancemtx[i][j] = ( 1.0 - distancemtx[i][j] / bunbo ) * 2.0;
1222	}
1223	}
1224
1225	hat2p = fopen( hat2file, "w" );
1226	if( !hat2p ) ErrorExit( "Cannot open hat2." );
1227	WriteHat2_pointer( hat2p, njob, name, distancemtx );
1228	fclose( hat2p );
1229
1230	fprintf( stderr, "##### writing hat3\n" );
1231	hat3p = fopen( "hat3", "w" );
1232	if( !hat3p ) ErrorExit( "Cannot open hat3." );
1233	ilim = njob-1;
1234	for( i=0; i<ilim; i++ )
1235	{
1236	for( j=i+1; j<njob; j++ )
1237	{
1238	for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next )
1239	{
1240	if( tmpptr->opt == -1.0 ) continue;
1241	fprintf( hat3p, "%d %d %d %7.5f %d %d %d %d k\n", i, j, tmpptr->overlapaa, tmpptr->opt, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2 );
1242	}
1243	}
1244	}
1245	fclose( hat3p );
1246	#if DEBUG
1247	fprintf( stderr, "calling FreeLocalHomTable\n" );
1248	#endif
1249	FreeLocalHomTable( localhomtable, njob );
1250	#if DEBUG
1251	fprintf( stderr, "done. FreeLocalHomTable\n" );
1252	#endif
1253	}
1254
1255	static void WriteOptions( FILE *fp )
1256	{
1257
1258	if( dorp == 'd' ) fprintf( fp, "DNA\n" );
1259	else
1260	{
1261	if ( scoremtx == 0 ) fprintf( fp, "JTT %dPAM\n", pamN );
1262	else if( scoremtx == 1 ) fprintf( fp, "BLOSUM %d\n", nblosum );
1263	else if( scoremtx == 2 ) fprintf( fp, "M-Y\n" );
1264	}
1265	fprintf( stderr, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
1266	if( use_fft ) fprintf( fp, "FFT on\n" );
1267
1268	fprintf( fp, "tree-base method\n" );
1269	if( tbrweight == 0 ) fprintf( fp, "unweighted\n" );
1270	else if( tbrweight == 3 ) fprintf( fp, "clustalw-like weighting\n" );
1271	if( tbitr \|\| tbweight )
1272	{
1273	fprintf( fp, "iterate at each step\n" );
1274	if( tbitr && tbrweight == 0 ) fprintf( fp, " unweighted\n" );
1275	if( tbitr && tbrweight == 3 ) fprintf( fp, " reversely weighted\n" );
1276	if( tbweight ) fprintf( fp, " weighted\n" );
1277	fprintf( fp, "\n" );
1278	}
1279
1280	fprintf( fp, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
1281
1282	if( alg == 'a' )
1283	fprintf( fp, "Algorithm A\n" );
1284	else if( alg == 'A' )
1285	fprintf( fp, "Algorithm A+\n" );
1286	else if( alg == 'S' )
1287	fprintf( fp, "Apgorithm S\n" );
1288	else if( alg == 'C' )
1289	fprintf( fp, "Apgorithm A+/C\n" );
1290	else
1291	fprintf( fp, "Unknown algorithm\n" );
1292
1293	if( use_fft )
1294	{
1295	fprintf( fp, "FFT on\n" );
1296	if( dorp == 'd' )
1297	fprintf( fp, "Basis : 4 nucleotides\n" );
1298	else
1299	{
1300	if( fftscore )
1301	fprintf( fp, "Basis : Polarity and Volume\n" );
1302	else
1303	fprintf( fp, "Basis : 20 amino acids\n" );
1304	}
1305	fprintf( fp, "Threshold of anchors = %d%%\n", fftThreshold );
1306	fprintf( fp, "window size of anchors = %dsites\n", fftWinSize );
1307	}
1308	else
1309	fprintf( fp, "FFT off\n" );
1310	fflush( fp );
1311	}
1312
1313
1314	int main( int argc, char *argv[] )
1315	{
1316	static int nlen[M];
1317	static char name, seq;
1318	static char mseq1, mseq2;
1319	static char **aseq;
1320	static char **bseq;
1321	static double *eff;
1322	static double *equiv;
1323	char **strfiles;
1324	char **chainids;
1325	int i;
1326	FILE *infp;
1327	char c;
1328	int alloclen;
1329
1330	arguments( argc, argv );
1331
1332	if( equivthreshold < 1 \|\| 9 < equivthreshold )
1333	{
1334	fprintf( stderr, "-t n, n must be 1..9\n" );
1335	exit( 1 );
1336	}
1337
1338	if( ( equivwinsize + 1 ) % 2 != 0 )
1339	{
1340	fprintf( stderr, "equivwinsize = %d\n", equivwinsize );
1341	fprintf( stderr, "It must be an odd number.\n" );
1342	exit( 1 );
1343	}
1344
1345	if( inputfile )
1346	{
1347	infp = fopen( inputfile, "r" );
1348	if( !infp )
1349	{
1350	fprintf( stderr, "Cannot open %s\n", inputfile );
1351	exit( 1 );
1352	}
1353	}
1354	else
1355	infp = stdin;
1356
1357	nlenmax = 10000; // tekitou
1358
1359	if( alg == 'R' )
1360	prepareash( infp, inputfile, &strfiles, &chainids, &seq, &mseq1, &mseq2, &equiv, &alloclen );
1361	else if( alg == 'T' )
1362	preparetmalign( infp, &strfiles, &chainids, &seq, &mseq1, &mseq2, &equiv, &alloclen );
1363
1364	fclose( infp );
1365
1366	name = AllocateCharMtx( njob, B+1 );
1367	aseq = AllocateCharMtx( njob, nlenmax*2+1 );
1368	bseq = AllocateCharMtx( njob, nlenmax*2+1 );
1369	eff = AllocateDoubleVec( njob );
1370
1371	for( i=0; i<njob; i++ )
1372	{
1373	fprintf( stderr, "str%d = %s-%s\n", i, strfiles[i], chainids[i] );
1374	}
1375
1376	if( njob < 1 )
1377	{
1378	fprintf( stderr, "No structure found.\n" );
1379	exit( 1 );
1380	}
1381	if( njob < 2 )
1382	{
1383	fprintf( stderr, "Only %d structure found.\n", njob );
1384	exit( 0 );
1385	}
1386	if( njob > M )
1387	{
1388	fprintf( stderr, "The number of structures must be < %d\n", M );
1389	fprintf( stderr, "Please try sequence-based methods for such large data.\n" );
1390	exit( 1 );
1391	}
1392
1393
1394
1395	#if 0
1396	readData( infp, name, nlen, seq );
1397	#endif
1398
1399	constants( njob, seq );
1400
1401	#if 0
1402	fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );
1403	#endif
1404
1405	initSignalSM();
1406
1407	initFiles();
1408
1409	WriteOptions( trap_g );
1410
1411	c = seqcheck( seq );
1412	if( c )
1413	{
1414	fprintf( stderr, "Illegal character %c\n", c );
1415	exit( 1 );
1416	}
1417
1418	// writePre( njob, name, nlen, seq, 0 );
1419
1420	for( i=0; i<njob; i++ ) eff[i] = 1.0;
1421
1422
1423	for( i=0; i<njob; i++ ) gappick0( bseq[i], seq[i] );
1424
1425	pairalign( name, nlen, bseq, aseq, mseq1, mseq2, equiv, eff, strfiles, chainids, alloclen );
1426
1427	fprintf( trap_g, "done.\n" );
1428	#if DEBUG
1429	fprintf( stderr, "closing trap_g\n" );
1430	#endif
1431	fclose( trap_g );
1432
1433	// writePre( njob, name, nlen, aseq, !contin );
1434	#if 0
1435	writeData( stdout, njob, name, nlen, aseq );
1436	#endif
1437	#if IODEBUG
1438	fprintf( stderr, "OSHIMAI\n" );
1439	#endif
1440	SHOWVERSION;
1441	return( 0 );
1442	}

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source: tags/arb-6.0/GDE/MAFFT/mafft-7.055-with-extensions/core/pairash.c

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