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source: tags/arb_5.5/CONVERTALN/embl.c

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Last change on this file was 5178, checked in by westram, 16 years ago
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1	#include <stdio.h>
2	#include <stdlib.h>
3	#include "convert.h"
4	#include "global.h"
5
6	extern int warning_out;
7
8	/* ----------------------------------------------------------
9	* Function init_pm_data().
10	* Init macke and embl data.
11	*/
12	void
13	init_em_data() {
14	/* void init_macke(), init_embl(); */
15
16	init_macke();
17	init_embl();
18	}
19	/* ------------------------------------------------------------
20	* Function init_embl().
21	* Initialize embl entry.
22	*/
23	void
24	init_embl() {
25
26	int indi;
27	/* void Freespace(); */
28	/* char Dupstr(); /
29
30	/* initialize embl format */
31	Freespace(&(data.embl.id));
32	Freespace(&(data.embl.dateu));
33	Freespace(&(data.embl.datec));
34	Freespace(&(data.embl.description));
35	Freespace(&(data.embl.os));
36	Freespace(&(data.embl.accession));
37	Freespace(&(data.embl.keywords));
38
39	for(indi=0; indi<data.embl.numofref; indi++) {
40	Freespace(&(data.embl.reference[indi].author));
41	Freespace(&(data.embl.reference[indi].title));
42	Freespace(&(data.embl.reference[indi].journal));
43	Freespace(&(data.embl.reference[indi].processing));
44	}
45	Freespace(&(data.embl.reference));
46	Freespace(&(data.embl.dr));
47	Freespace(&(data.embl.comments.orginf.source));
48	Freespace(&(data.embl.comments.orginf.cc));
49	Freespace(&(data.embl.comments.orginf.formname));
50	Freespace(&(data.embl.comments.orginf.nickname));
51	Freespace(&(data.embl.comments.orginf.commname));
52	Freespace(&(data.embl.comments.orginf.hostorg));
53	Freespace(&(data.embl.comments.seqinf.RDPid));
54	Freespace(&(data.embl.comments.seqinf.gbkentry));
55	Freespace(&(data.embl.comments.seqinf.methods));
56	Freespace(&(data.embl.comments.others));
57
58	data.embl.id=Dupstr("\n");
59	data.embl.dateu=Dupstr("\n");
60	data.embl.datec=Dupstr("\n");
61	data.embl.description=Dupstr("\n");
62	data.embl.os=Dupstr("\n");
63	data.embl.accession=Dupstr("\n");
64	data.embl.keywords=Dupstr("\n");
65	data.embl.dr=Dupstr("\n");
66	data.embl.numofref=0;
67	data.embl.reference=NULL;
68	data.embl.comments.orginf.exist=0;
69	data.embl.comments.orginf.source=Dupstr("\n");
70	data.embl.comments.orginf.cc=Dupstr("\n");
71	data.embl.comments.orginf.formname=Dupstr("\n");
72	data.embl.comments.orginf.nickname=Dupstr("\n");
73	data.embl.comments.orginf.commname=Dupstr("\n");
74	data.embl.comments.orginf.hostorg=Dupstr("\n");
75	data.embl.comments.seqinf.exist=0;
76	data.embl.comments.seqinf.RDPid=Dupstr("\n");
77	data.embl.comments.seqinf.gbkentry=Dupstr("\n");
78	data.embl.comments.seqinf.methods=Dupstr("\n");
79	data.embl.comments.others=NULL;
80	data.embl.comments.seqinf.comp5=' ';
81	data.embl.comments.seqinf.comp3=' ';
82	}
83	/* ---------------------------------------------------------------
84	* Function embl_in().
85	* Read in one embl entry.
86	*/
87	char
88	embl_in(fp)
89	FILE_BUFFER fp;
90	{
91	char line[LINENUM], key[TOKENNUM];
92	char *eof, eoen;
93	/* char embl_date(); /
94	/* char embl_version(); /
95	/* char embl_comments(), embl_origin(); */
96	/* char embl_skip_unidentified(); /
97	/* char Dupstr(), temp; */
98	/* void embl_key_word(), warning(), error(), Append_char(); */
99	/* void replace_entry(), embl_verify_title(); */
100	int refnum;
101
102	eoen=' '; /* end-of-entry, set to be 'y' after '//' is read */
103
104	for(eof=Fgetline(line, LINENUM, fp); eof!=NULL&&eoen!='y'; ) {
105	if(Lenstr(line)<=1) {
106	eof=Fgetline(line, LINENUM, fp);
107	continue; /* empty line, skip */
108	}
109
110	embl_key_word(line, 0, key, TOKENNUM);
111	eoen='n';
112
113	if((Cmpstr(key, "ID"))==EQ) {
114	eof = embl_one_entry(line, fp,
115	&(data.embl.id), key);
116
117	} else if((Cmpstr(key, "DT"))==EQ) {
118	eof = embl_date(line, fp);
119
120	} else if((Cmpstr(key, "DE"))==EQ) {
121	eof = embl_one_entry(line, fp,
122	&(data.embl.description), key);
123
124	} else if((Cmpstr(key, "OS"))==EQ) {
125	eof = embl_one_entry(line, fp,
126	&(data.embl.os), key);
127
128	} else if((Cmpstr(key, "AC"))==EQ) {
129	eof = embl_one_entry(line, fp,
130	&(data.embl.accession), key);
131
132	} else if((Cmpstr(key, "KW"))==EQ) {
133	eof = embl_one_entry(line, fp,
134	&(data.embl.keywords), key);
135
136	/* correct missing '.' */
137	if(Lenstr(data.embl.keywords)<=1) {
138	replace_entry(&(data.embl.keywords), ".\n");
139	} else Append_char(&(data.embl.keywords), '.');
140
141	} else if((Cmpstr(key, "DR"))==EQ) {
142	eof = embl_one_entry(line, fp,
143	&(data.embl.dr), key);
144
145	} else if((Cmpstr(key, "RA"))==EQ) {
146
147	refnum = data.embl.numofref-1;
148	eof = embl_one_entry(line, fp,
149	&(data.embl.reference[refnum].author), key);
150	Append_char
151	(&(data.embl.reference[refnum].author), ';');
152
153	} else if((Cmpstr(key, "RT"))==EQ) {
154
155	refnum = data.embl.numofref-1;
156	eof = embl_one_entry(line, fp,
157	&(data.embl.reference[refnum].title), key);
158
159	/* Check missing '"' at the both ends */
160	embl_verify_title(refnum);
161
162	} else if((Cmpstr(key, "RL"))==EQ) {
163
164	refnum = data.embl.numofref-1;
165	eof = embl_one_entry(line, fp,
166	&(data.embl.reference[refnum].journal), key);
167	Append_char
168	(&(data.embl.reference[refnum].journal), '.');
169
170	} else if((Cmpstr(key, "RP"))==EQ) {
171
172	refnum = data.embl.numofref-1;
173	eof = embl_one_entry(line, fp,
174	&(data.embl.reference[refnum].processing), key);
175
176	} else if((Cmpstr(key, "RN"))==EQ) {
177
178	eof = embl_version(line, fp);
179
180	} else if((Cmpstr(key, "CC"))==EQ) {
181
182	eof = embl_comments(line, fp);
183
184	} else if((Cmpstr(key, "SQ"))==EQ) {
185
186	eof = embl_origin(line, fp);
187	eoen = 'y';
188
189	} else { /* unidentified key word */
190	eof = embl_skip_unidentified(key, line, fp);
191	}
192	/* except "ORIGIN", at the end of all the other cases,
193	* a new line has already read in, so no further read
194	* is necessary */
195
196	} /* for loop to read an entry line by line */
197
198	if(eoen=='n')
199	error(83, "Reach EOF before one entry is read, Exit");
200
201	if(eof==NULL) return(EOF);
202	else return(EOF+1);
203
204	}
205	/* ---------------------------------------------------------------
206	* Function embl_in_id().
207	* Read in one embl entry.
208	*/
209	char
210	embl_in_id(fp)
211	FILE_BUFFER fp;
212	{
213	char line[LINENUM], key[TOKENNUM];
214	char *eof, eoen;
215	/* char embl_one_entry(), embl_origin(); */
216	/* char embl_skip_unidentified(); /
217	/* void embl_key_word(), warning(), error(); */
218	/* int Lenstr(); */
219
220	eoen=' ';
221	/* end-of-entry, set to be 'y' after '//' is read */
222
223	for(eof=Fgetline(line, LINENUM, fp); eof!=NULL&&eoen!='y'; )
224	{
225	if(Lenstr(line)<=1) {
226	eof=Fgetline(line, LINENUM, fp);
227	continue; /* empty line, skip */
228	}
229
230	embl_key_word(line, 0, key, TOKENNUM);
231	eoen='n';
232
233	if((Cmpstr(key, "ID"))==EQ) {
234	eof = embl_one_entry(line, fp,
235	&(data.embl.id), key);
236	} else if((Cmpstr(key, "SQ"))==EQ) {
237	eof = embl_origin(line, fp);
238	eoen = 'y';
239	} else { /* unidentified key word */
240	eof = embl_skip_unidentified(key, line, fp);
241	}
242	/* except "ORIGIN", at the end of all the other cases,
243	a new line has already read in, so no further read
244	is necessary */
245
246	} /* for loop to read an entry line by line */
247
248	if(eoen=='n')
249	error(84, "Reach EOF before one entry is read, Exit");
250
251	if(eof==NULL) return(EOF);
252	else return(EOF+1);
253
254	}
255	/* ----------------------------------------------------------------
256	* Function embl_key_word().
257	* Get the key_word from line beginning at index.
258	*/
259	void
260	embl_key_word(line, index, key, length)
261	char *line;
262	int index;
263	char *key;
264	int length; /* max size of key word */
265	{
266	int indi, indj;
267
268	if(line==NULL) { key[0]='\0'; return; }
269	for(indi=index, indj=0; (index-indi)<length&&line[indi]!=' '
270	&&line[indi]!='\t'&&line[indi]!='\n'&&line[indi]!='\0';
271	indi++, indj++)
272	key[indj] = line[indi];
273	key[indj] = '\0';
274	}
275	/* ------------------------------------------------------------
276	* Function embl_check_blanks().
277	* Check if there is (numb) blanks at beginning of line.
278	*/
279	int
280	embl_check_blanks(line, numb)
281	char *line;
282	int numb;
283	{
284	int blank=1, indi, indk;
285
286	for(indi=0; blank&&indi<numb; indi++) {
287	if(line[indi]!=' '&&line[indi]!='\t') blank=0;
288	if(line[indi]=='\t') {
289	indk=indi/8+1; indi=8*indk+1;
290	}
291	}
292
293	return(blank);
294	}
295	/* ----------------------------------------------------------------
296	* Function embl_continue_line().
297	* if there are (numb) blanks at the beginning of line,
298	* it is a continue line of the current command.
299	*/
300	char
301	*embl_continue_line(pattern, string, line, fp)
302	char pattern, string, line;
303	FILE_BUFFER fp;
304	{
305	int ind;
306	/* int embl_check_blanks(), Skip_white_space(); */
307	char key[TOKENNUM], *eof, temp[LINENUM];
308	/* void Cpystr(), embl_key_word(), Append_rp_eoln(); */
309
310	/* check continue lines */
311	for(eof=Fgetline(line, LINENUM, fp);
312	eof!=NULL; eof=Fgetline(line, LINENUM, fp)) {
313
314	if(Lenstr(line)<=1) continue;
315
316	embl_key_word(line, 0, key, TOKENNUM);
317
318	if(Cmpstr(pattern, key)!=EQ) break;
319
320	/* remove end-of-line, if there is any */
321	ind=Skip_white_space(line, p_nonkey_start);
322	Cpystr(temp, (line+ind));
323	Append_rp_eoln(string, temp);
324
325	} /* end of continue line checking */
326
327	return(eof);
328	}
329	/* --------------------------------------------------------------
330	* Function embl_one_entry().
331	* Read in one embl entry lines.
332	*/
333	char
334	*embl_one_entry(line, fp, entry, key)
335	char *line;
336	FILE_BUFFER fp;
337	char *entry, key;
338	{
339	int index;
340	char *eof;
341	/* void error(), replace_entry(); */
342
343	index = Skip_white_space(line, p_nonkey_start);
344	replace_entry(entry, line+index);
345	eof = (char*)embl_continue_line(key, entry, line, fp);
346
347	return(eof);
348	}
349	/* ---------------------------------------------------------------
350	* Function embl_verify_title().
351	* Verify title.
352	*/
353	void
354	embl_verify_title(refnum)
355	int refnum;
356	{
357	int len;
358	char *temp;
359	/* void Append(), Append_char(), replace_entry(); */
360
361	Append_char(&(data.embl.reference[refnum].title), ';');
362
363	len=Lenstr(data.embl.reference[refnum].title);
364	if(len>2&&(data.embl.reference[refnum].title[0]!='"'
365	\|\|data.embl.reference[refnum].title[len-3]!='"')) {
366	if(data.embl.reference[refnum].title[0]!='"')
367	temp=(char*)Dupstr("\"");
368	else temp=(char*)Dupstr("");
369	Append(&temp, data.embl.reference[refnum].title);
370	if((len>2&&data.embl.reference[refnum].title[len-3]
371	!='"'))
372	{
373	len=Lenstr(temp);
374	temp[len-2]='"';
375	Append_char(&temp, ';');
376	}
377	replace_entry(&(data.embl.reference[refnum].title),
378	temp);
379	}
380	}
381	/* --------------------------------------------------------------
382	* Function embl_date().
383	* Read in embl DATE lines.
384	*/
385	char
386	*embl_date(line, fp)
387	char *line;
388	FILE_BUFFER fp;
389	{
390	int index;
391	char *eof, key[TOKENNUM];
392	/* void error(), embl_key_word(), replace_entry(); */
393	/* void warning(); */
394
395	index = Skip_white_space(line, p_nonkey_start);
396	replace_entry(&(data.embl.dateu), line+index);
397
398	eof = Fgetline(line, LINENUM, fp);
399	embl_key_word(line, 0, key, TOKENNUM);
400	if((Cmpstr(key, "DT"))==EQ) {
401	index = Skip_white_space(line, p_nonkey_start);
402	replace_entry(&(data.embl.datec), line+index);
403	/* skip the rest of DT lines */
404	do {
405	eof = Fgetline(line, LINENUM, fp);
406	embl_key_word(line, 0, key, TOKENNUM);
407	} while(eof!=NULL&&Cmpstr(key, "DT")==EQ);
408	return(eof);
409	} else {
410	/* always expect more than two DT lines */
411	warning(33, "one DT line is missing");
412	return(eof);
413	}
414	}
415	/* --------------------------------------------------------------
416	* Function embl_version().
417	* Read in embl RN lines.
418	*/
419	char
420	*embl_version(line, fp)
421	char *line;
422	FILE_BUFFER fp;
423	{
424	int index;
425	char *eof;
426	/* char Reallocspace(), Fgetline(); */
427
428	index = Skip_white_space(line, p_nonkey_start);
429	if(data.embl.numofref==0) {
430	data.embl.numofref = 1;
431	data.embl.reference = (Emblref)calloc(1,sizeof(Emblref)1);
432	data.embl.reference[0].author = Dupstr("");
433	data.embl.reference[0].title = Dupstr("");
434	data.embl.reference[0].journal = Dupstr("");
435	data.embl.reference[0].processing = Dupstr("");
436	} else {
437	data.embl.numofref++;
438	data.embl.reference = (Emblref)Reallocspace(data.embl.reference, sizeof(Emblref)(data.embl.numofref));
439	data.embl.reference[data.embl.numofref-1].author = Dupstr("");
440	data.embl.reference[data.embl.numofref-1].title = Dupstr("");
441	data.embl.reference[data.embl.numofref-1].journal = Dupstr("");
442	data.embl.reference[data.embl.numofref-1].processing = Dupstr("");
443	}
444	eof = Fgetline(line, LINENUM, fp);
445	return(eof);
446	}
447	/* --------------------------------------------------------------
448	* Function embl_comments().
449	* Read in embl comment lines.
450	*/
451	char
452	*embl_comments(line, fp)
453	char *line;
454	FILE_BUFFER fp;
455	{
456	int index, offset;
457	/* int Skip_white_space(); */
458	char *eof;
459	char key[TOKENNUM];
460	/* char Dupstr(); /
461	/* void Append(); */
462
463	for(;line[0]=='C'&&line[1]=='C';) {
464
465	index = Skip_white_space(line, 5);
466	offset = embl_comment_key(line+index, key);
467	index = Skip_white_space(line, index+offset);
468	if(Cmpstr(key, "Source of strain:")==EQ) {
469	eof = embl_one_comment_entry
470	(fp, &(data.embl.comments.orginf.source),
471	line, index);
472
473	} else if(Cmpstr(key, "Culture collection:")==EQ) {
474
475	eof = embl_one_comment_entry
476	(fp, &(data.embl.comments.orginf.cc),
477	line, index);
478
479	} else if(Cmpstr(key, "Former name:")==EQ) {
480
481	eof = embl_one_comment_entry
482	(fp, &(data.embl.comments.orginf.formname),
483	line, index);
484
485	} else if(Cmpstr(key, "Alternate name:")==EQ) {
486
487	eof = embl_one_comment_entry
488	(fp, &(data.embl.comments.orginf.nickname),
489	line, index);
490
491	} else if(Cmpstr(key, "Common name:")==EQ) {
492
493	eof = embl_one_comment_entry
494	(fp, &(data.embl.comments.orginf.commname),
495	line, index);
496
497	} else if(Cmpstr(key, "Host organism:")==EQ) {
498
499	eof = embl_one_comment_entry
500	(fp, &(data.embl.comments.orginf.hostorg),
501	line, index);
502
503	} else if(Cmpstr(key, "RDP ID:")==EQ) {
504	eof = embl_one_comment_entry
505	(fp, &(data.embl.comments.seqinf.RDPid),
506	line, index);
507
508	} else if(Cmpstr(key,
509	"Corresponding GenBank entry:")==EQ) {
510
511	eof = embl_one_comment_entry
512	(fp, &(data.embl.comments.seqinf.gbkentry),
513	line, index);
514
515	} else if(Cmpstr(key, "Sequencing methods:")==EQ) {
516
517	eof = embl_one_comment_entry
518	(fp, &(data.embl.comments.seqinf.methods),
519	line, index);
520
521	} else if(Cmpstr(key, "5' end complete:")==EQ) {
522
523	sscanf(line+index, "%s", key);
524	if(key[0]=='Y')
525	data.embl.comments.seqinf.comp5 = 'y';
526	else data.embl.comments.seqinf.comp5 = 'n';
527
528	eof=Fgetline(line, LINENUM, fp);
529
530	} else if(Cmpstr(key, "3' end complete:")==EQ) {
531
532	sscanf(line+index, "%s", key);
533	if(key[0]=='Y')
534	data.embl.comments.seqinf.comp3 = 'y';
535	else data.embl.comments.seqinf.comp3 = 'n';
536
537	eof=Fgetline(line, LINENUM, fp);
538
539	} else if(Cmpstr(key,
540	"Sequence information ")==EQ) {
541
542	/* do nothing */
543	data.embl.comments.seqinf.exist = 1;
544
545	eof=Fgetline(line, LINENUM, fp);
546
547	} else if(Cmpstr(key, "Organism information")==EQ) {
548
549	/* do nothing */
550	data.embl.comments.orginf.exist = 1;
551
552	eof=Fgetline(line, LINENUM, fp);
553
554	} else { /* other comments */
555
556	if(data.embl.comments.others == NULL) {
557	data.embl.comments.others
558	=(char*)Dupstr(line+5);
559
560	} else Append(&(data.embl.comments.others),
561	line+5);
562	eof=Fgetline(line, LINENUM, fp);
563
564	}
565	}
566	return(eof);
567	}
568	/* ----------------------------------------------------------------
569	* Function embl_skip_unidentified().
570	* if there are (numb) blanks at the beginning of line,
571	* it is a continue line of the current command.
572	*/
573	char
574	*embl_skip_unidentified(pattern, line, fp)
575	char pattern, line;
576	FILE_BUFFER fp;
577	{
578	/* int Lenstr(), Cmpstr(); */
579	char *eof;
580	char key[TOKENNUM];
581	/* void embl_key_word(); */
582
583	/* check continue lines */
584	for(eof=Fgetline(line, LINENUM, fp);
585	eof!=NULL; eof=Fgetline(line, LINENUM, fp)) {
586	embl_key_word(line, 0, key, TOKENNUM);
587	if(Cmpstr(key, pattern)!=EQ) break;
588	} /* end of continue line checking */
589	return(eof);
590	}
591	/* -------------------------------------------------------------
592	* Function embl_comment_key().
593	* Get the subkey_word in comment lines beginning
594	* at index.
595	*/
596	int
597	embl_comment_key(line, key)
598	char *line;
599	char *key;
600	{
601	int indi, indj;
602
603	if(line==NULL) { key[0]='\0'; return(0); }
604
605	for(indi=indj=0;
606	line[indi]!=':'&&line[indi]!='\t'&&line[indi]!='\n'
607	&&line[indi]!='\0'&&line[indi]!='('; indi++, indj++)
608	key[indj] = line[indi];
609
610	if(line[indi]==':') key[indj++] = ':';
611
612	key[indj] = '\0';
613
614	return(indi+1);
615	}
616	/* ------------------------------------------------------------
617	* Function embl_one_comment_entry().
618	* Read in one embl sub-entry in comments lines.
619	* If not RDP defined comment, should not call
620	* this function.
621	*/
622	char *embl_one_comment_entry(fp, datastring, line, start_index)
623	FILE_BUFFER fp;
624	char *datastring, line;
625	int start_index;
626	{
627	int index;
628	/* int Skip_white_space(), Lenstr(), Blank_num(); */
629	char *eof, temp[LINENUM];
630	/* char eof, Fgetline(), Dupstr(), temp[LINENUM]; /
631	/* void replace_entry(), Cpystr(), Append_rp_eoln(); */
632
633	index = Skip_white_space(line, start_index);
634	replace_entry(datastring, line+index);
635
636	/* check continue lines */
637	for(eof=Fgetline(line, LINENUM, fp);
638	eof!=NULL&&line[0]=='C'&&line[1]=='C'
639	&&Blank_num(line+2)>=COMMCNINDENT+COMMSKINDENT;
640	eof=Fgetline(line, LINENUM, fp)) {
641
642	/* remove end-of-line, if there is any */
643	index=Skip_white_space(line, p_nonkey_start+COMMSKINDENT+COMMCNINDENT);
644	Cpystr(temp, (line+index));
645	Append_rp_eoln(datastring, temp);
646
647	} /* end of continue line checking */
648
649	return eof;
650	}
651	/* --------------------------------------------------------------
652	* Function embl_origin().
653	* Read in embl sequence data.
654	*/
655	char
656	*embl_origin(line, fp)
657	char *line;
658	FILE_BUFFER fp;
659	{
660	char *eof;
661	int index;
662
663	data.seq_length = 0;
664	/* read in whole sequence data */
665	for(eof=Fgetline(line, LINENUM, fp);
666	eof!=NULL&&line[0]!='/'&&line[1]!='/';
667	eof=Fgetline(line, LINENUM, fp))
668	{
669	for(index=5; line[index]!='\n'&&line[index]!='\0';
670	index++) {
671	if(line[index]!=' '
672	&&data.seq_length>=data.max) {
673	data.max += 100;
674	data.sequence = (char*)
675	Reallocspace(data.sequence,
676	(unsigned)(sizeof(char)*data.max));
677	}
678	if(line[index]!=' ')
679	data.sequence[data.seq_length++]
680	= line[index];
681	}
682	data.sequence[data.seq_length] = '\0';
683	}
684
685	return(eof);
686	}
687	/* ----------------------------------------------------------------
688	* Function embl_out().
689	* Output EMBL data.
690	*/
691	void embl_out(fp)
692	FILE *fp;
693	{
694	/* int Lenstr(); */
695	/* int base_a, base_t, base_g, base_c, base_other; */
696	int indi /, indj, indk, len/;
697	/* void embl_print_lines(), embl_out_comments(); */
698	/* void embl_out_origin(); */
699
700	if(Lenstr(data.embl.id)>1)
701	fprintf(fp, "ID %sXX\n", data.embl.id);
702	if(Lenstr(data.embl.accession)>1) {
703	embl_print_lines(fp, "AC", data.embl.accession, SEPNODEFINED, "");
704	fprintf(fp, "XX\n");
705	}
706
707	/* Date */
708	if(Lenstr(data.embl.dateu)>1)
709	fprintf(fp, "DT %s", data.embl.dateu);
710	if(Lenstr(data.embl.datec)>1)
711	fprintf(fp, "DT %sXX\n", data.embl.datec);
712	if(Lenstr(data.embl.description)>1) {
713	embl_print_lines(fp, "DE", data.embl.description, SEPNODEFINED, "");
714	fprintf(fp, "XX\n");
715	}
716
717	if(Lenstr(data.embl.keywords)>1) {
718	embl_print_lines(fp, "KW", data.embl.keywords, SEPDEFINED, ";");
719	fprintf(fp, "XX\n");
720	}
721
722	if(Lenstr(data.embl.os)>1) {
723	embl_print_lines(fp, "OS", data.embl.os, SEPNODEFINED, "");
724	fprintf(fp, "OC No information.\n");
725	fprintf(fp, "XX\n");
726	}
727
728	/* Reference */
729	for(indi=0; indi<data.embl.numofref; indi++) {
730	fprintf(fp, "RN [%d]\n", indi+1);
731	if(Lenstr(data.embl.reference[indi].processing)>1)
732	fprintf(fp, "RP %s",
733	data.embl.reference[indi].processing);
734	if(Lenstr(data.embl.reference[indi].author)>1)
735	embl_print_lines(fp, "RA", data.embl.reference[indi].author, SEPDEFINED, ",");
736	if(Lenstr(data.embl.reference[indi].title)>1)
737	embl_print_lines(fp, "RT", data.embl.reference[indi].title, SEPNODEFINED, "");
738	else fprintf(fp, "RT ;\n");
739	if(Lenstr(data.embl.reference[indi].journal)>1)
740	embl_print_lines(fp, "RL", data.embl.reference[indi].journal, SEPNODEFINED, "");
741	fprintf(fp, "XX\n");
742	}
743
744	if(Lenstr(data.embl.dr)>1) {
745	embl_print_lines(fp, "DR", data.embl.dr, SEPNODEFINED, "");
746	fprintf(fp, "XX\n");
747	}
748
749	embl_out_comments(fp);
750	embl_out_origin(fp);
751	}
752	/* ----------------------------------------------------------------
753	* Function embl_print_lines().
754	* Print EMBL entry and wrap around if line over
755	* EMBLMAXCHAR.
756	*/
757	void embl_print_lines(fp, key, Data, flag, separators)
758	FILE *fp;
759	const char *key;
760	char *Data;
761	int flag;
762	const char *separators;
763	{
764	int indi, indj, indk, len;
765	int ibuf;
766
767	len = Lenstr(Data)-1;
768	/* indi: first char of the line */
769	/* indj: num of char, excluding the first char, of the line */
770	for(indi=0; indi<len; indi+=(indj+1)) {
771	indj=EMBLMAXCHAR;
772	if((Lenstr(Data+indi))>EMBLMAXCHAR) {
773
774	ibuf = indj;
775
776	/* searching for proper termination of a line */
777	for(;indj>0
778	&&((!flag&&!last_word(Data[indi+indj]))
779	\|\|(flag&&!is_separator
780	(Data[indi+indj], separators)));
781	indj--) ;
782
783	if(indj==0) indj=ibuf;
784	else if(Data[indi+indj+1]==' ') indj++;
785
786	fprintf(fp, "%s ", key);
787
788	for(indk=0; indk<indj; indk++)
789	fprintf(fp, "%c", Data[indi+indk]);
790
791	/* leave out the last space, if there is any */
792	if(Data[indi+indj]!=' ')
793	fprintf(fp, "%c", Data[indi+indj]);
794
795	fprintf(fp, "\n");
796
797	} else fprintf(fp, "%s %s", key, Data+indi);
798	}
799	}
800	/* -------------------------------------------------------
801	* Function embl_out_comments().
802	* Print out the comments part of EMBL format.
803	*/
804	void
805	embl_out_comments(fp)
806	FILE *fp;
807	{
808	int indi, len;
809	/* void embl_print_comment(); */
810
811	if(data.embl.comments.orginf.exist==1) {
812	fprintf(fp, "CC Organism information\n");
813
814	if(Lenstr(data.embl.comments.orginf.source)>1)
815	embl_print_comment(fp, "Source of strain: ", data.embl.comments.orginf.source, COMMSKINDENT, COMMCNINDENT);
816
817	if(Lenstr(data.embl.comments.orginf.cc)>1)
818	embl_print_comment(fp, "Culture collection: ", data.embl.comments.orginf.cc, COMMSKINDENT, COMMCNINDENT);
819
820	if(Lenstr(data.embl.comments.orginf.formname)>1)
821	embl_print_comment(fp, "Former name: ", data.embl.comments.orginf.formname, COMMSKINDENT, COMMCNINDENT);
822
823	if(Lenstr(data.embl.comments.orginf.nickname)>1)
824	embl_print_comment(fp, "Alternate name: ", data.embl.comments.orginf.nickname, COMMSKINDENT, COMMCNINDENT);
825
826	if(Lenstr(data.embl.comments.orginf.commname)>1)
827	embl_print_comment(fp, "Common name: ", data.embl.comments.orginf.commname, COMMSKINDENT, COMMCNINDENT);
828
829	if(Lenstr(data.embl.comments.orginf.hostorg)>1)
830	embl_print_comment(fp, "Host organism: ", data.embl.comments.orginf.hostorg, COMMSKINDENT, COMMCNINDENT);
831
832	} /* organism information */
833
834	if(data.embl.comments.seqinf.exist==1) {
835
836	fprintf(fp,
837	"CC Sequence information (bases 1 to %d)\n",
838	data.seq_length);
839
840	if(Lenstr(data.embl.comments.seqinf.RDPid)>1)
841	embl_print_comment(fp, "RDP ID: ",
842	data.embl.comments.seqinf.RDPid,
843	COMMSKINDENT, COMMCNINDENT);
844
845	if(Lenstr(data.embl.comments.seqinf.gbkentry)>1)
846	embl_print_comment(fp, "Corresponding GenBank entry: ",
847	data.embl.comments.seqinf.gbkentry,
848	COMMSKINDENT, COMMCNINDENT);
849
850	if(Lenstr(data.embl.comments.seqinf.methods)>1)
851	embl_print_comment(fp, "Sequencing methods: ",
852	data.embl.comments.seqinf.methods,
853	COMMSKINDENT, COMMCNINDENT);
854
855	if(data.embl.comments.seqinf.comp5=='n')
856	fprintf(fp,
857	"CC 5' end complete: No\n");
858
859	else if(data.embl.comments.seqinf.comp5=='y')
860	fprintf(fp,
861	"CC 5' end complete: Yes\n");
862
863	if(data.embl.comments.seqinf.comp3=='n')
864	fprintf(fp,
865	"CC 3' end complete: No\n");
866
867	else if(data.embl.comments.seqinf.comp3=='y')
868	fprintf(fp,
869	"CC 3' end complete: Yes\n");
870
871	} /* sequence information */
872
873	if(Lenstr(data.embl.comments.others)>1) {
874	for(indi=0, len=Lenstr(data.embl.comments.others);
875	indi<len; indi++){
876	if((indi>0&&data.embl.comments.others[indi-1]=='\n')
877	\|\|indi==0)
878	fprintf(fp, "CC ");
879	fprintf(fp, "%c",
880	data.embl.comments.others[indi]);
881	}
882	fprintf(fp, "XX\n");
883	}
884	}
885	/* --------------------------------------------------------------
886	* Fucntion embl_print_comment().
887	* Print one embl comment line, wrap around if over
888	* column 80.
889	*/
890	void embl_print_comment(fp, key, string, offset, indent)
891	FILE *fp;
892	const char *key;
893	char *string;
894	int offset, indent;
895	{
896	int first_time=1, indi, indj, indk, indl;
897	int len;
898
899	len = Lenstr(string)-1;
900	for(indi=0; indi<len; indi+=(indj+1)) {
901
902	if(first_time)
903	indj=EMBLMAXCHAR-offset-Lenstr(key)-1;
904	else indj=EMBLMAXCHAR-offset-indent-1;
905
906	fprintf(fp, "CC ");
907
908	if(!first_time) {
909	for(indl=0; indl<(offset+indent); indl++)
910	fprintf(fp, " ");
911	} else {
912	for(indl=0; indl<offset; indl++)
913	fprintf(fp, " ");
914	fprintf(fp, "%s", key);
915	first_time = 0;
916	}
917	if(Lenstr(string+indi)>indj) {
918
919	/* search for proper termination of a line */
920	for(; indj>=0&&!last_word(string[indj+indi]);
921	indj--) ;
922
923	/* print left margine */
924	if(string[indi]==' ') indk = 1;
925	else indk = 0;
926
927	for(; indk<indj; indk++)
928	fprintf(fp, "%c", string[indi+indk]);
929
930	/* leave out the last space, if there is any */
931	if(string[indi+indj]!=' ')
932	fprintf(fp, "%c", string[indi+indj]);
933	fprintf(fp, "\n");
934
935	} else fprintf(fp, "%s", string+indi);
936
937	} /* for each char */
938	}
939	/* -----------------------------------------------------
940	* Function embl_out_origin().
941	* Print out the sequence data of EMBL format.
942	*/
943	void
944	embl_out_origin(fp)
945	FILE *fp;
946	{
947	int base_a, base_c, base_t, base_g, base_other;
948	int indi, indj, indk;
949	/* void count_base(); */
950
951	/* print seq data */
952	count_base(&base_a, &base_t, &base_g, &base_c, &base_other);
953
954	fprintf(fp,
955	"SQ Sequence %d BP; %d A; %d C; %d G; %d T; %d other;\n",
956	data.seq_length, base_a, base_c, base_g, base_t, base_other);
957
958	for(indi=0, indj=0, indk=1; indi<data.seq_length; indi++)
959	{
960	if((indk % 60)==1) fprintf(fp, " ");
961	fprintf(fp, "%c", data.sequence[indi]);
962	indj++;
963	if((indk % 60)==0) { fprintf(fp, "\n"); indj=0; }
964	else if(indj==10&&indi!=(data.seq_length-1))
965	{ fprintf(fp, " "); indj=0; }
966	indk++;
967	}
968	if((indk % 60)==1) fprintf(fp, "//\n");
969	else fprintf(fp, "\n//\n");
970	}
971	/* ----------------------------------------------------------
972	* Function embl_to_macke().
973	* Convert from Embl format to Macke format.
974	*/
975	void
976	embl_to_macke(inf, outf, format)
977	char inf, outf;
978	int format;
979	{
980	FILE IFP, ofp;
981	FILE_BUFFER ifp;
982	char temp[TOKENNUM];
983	int indi, total_num;
984
985	if((IFP=fopen(inf, "r"))==NULL) {
986	sprintf(temp,
987	"Cannot open input file %s, exit\n", inf);
988	error(98, temp);
989	}
990	ifp = create_FILE_BUFFER(inf, IFP);
991	if(Lenstr(outf) <= 0) ofp = stdout;
992	else if((ofp=fopen(outf, "w"))==NULL) {
993	sprintf(temp,
994	"Cannot open output file %s, exit\n", outf);
995	error(97, temp);
996	}
997
998	init();
999	/* macke format seq irelenvant header */
1000	macke_out_header(ofp);
1001	for(indi=0; indi<3; indi++) {
1002	FILE_BUFFER_rewind(ifp);
1003	init_seq_data();
1004	init_em_data();
1005	while(embl_in(ifp)!=EOF) {
1006	data.numofseq++;
1007	if(etom()) {
1008	/* convert from embl form to macke form */
1009	switch(indi) {
1010	case 0:
1011	/* output seq display format */
1012	macke_out0(ofp, format);
1013	break;
1014	case 1:
1015	/* output seq information */
1016	macke_out1(ofp);
1017	break;
1018	case 2:
1019	/* output seq data */
1020	macke_out2(ofp);
1021	break;
1022	default: ;
1023	}
1024	} else error(4,
1025	"Conversion from embl to macke fails, Exit");
1026	init_em_data();
1027	}
1028	total_num = data.numofseq;
1029	if(indi==0) {
1030	fprintf(ofp, "#-\n");
1031	/* no warning messages for next loop */
1032	warning_out = 0;
1033	}
1034	} /* for each seq; loop */
1035
1036	warning_out = 1;
1037
1038	#ifdef log
1039	fprintf(stderr, "Total %d sequences have been processed\n",
1040	total_num);
1041	#endif
1042	}
1043	/* ------------------------------------------------------------
1044	* Function etom().
1045	* Convert from embl format to Macke format.
1046	*/
1047	int etom() {
1048	/* void init_genbank(); */
1049	/* int etog(), gtom(); */
1050
1051	init_genbank();
1052	if (etog()) return gtom();
1053	return 0;
1054	}
1055	/* -------------------------------------------------------------
1056	* Function embl_to_embl().
1057	* Print out EMBL data.
1058	*/
1059	void
1060	embl_to_embl(inf, outf)
1061	char inf, outf;
1062	{
1063	FILE IFP, ofp;
1064	FILE_BUFFER ifp;
1065	char temp[TOKENNUM];
1066
1067	if((IFP=fopen(inf, "r"))==NULL) {
1068	sprintf(temp,
1069	"Cannot open input file %s\n", inf);
1070	error(27, temp);
1071	}
1072	ifp = create_FILE_BUFFER(inf, IFP);
1073	if(Lenstr(outf) <= 0) ofp = stdout;
1074	else if((ofp=fopen(outf, "w"))==NULL) {
1075	sprintf(temp,
1076	"Cannot open output file %s\n", outf);
1077	error(28, temp);
1078	}
1079	init();
1080	init_seq_data();
1081	init_embl();
1082
1083	#ifdef log
1084	fprintf(stderr, "Start converting...\n");
1085	#endif
1086
1087	while(embl_in(ifp)!=EOF) {
1088	data.numofseq++;
1089	embl_out(ofp);
1090	init_embl();
1091	}
1092
1093	#ifdef log
1094	fprintf(stderr,
1095	"Total %d sequences have been processed\n",
1096	data.numofseq);
1097	#endif
1098
1099	}
1100	/* -------------------------------------------------------------
1101	* Function embl_to_genbank().
1102	* Convert from EMBL format to genbank format.
1103	*/
1104	void
1105	embl_to_genbank(inf, outf)
1106	char inf, outf;
1107	{
1108	FILE IFP, ofp;
1109	FILE_BUFFER ifp;
1110	char temp[TOKENNUM];
1111
1112	if((IFP=fopen(inf, "r"))==NULL) {
1113	sprintf(temp, "Cannot open input file %s\n", inf);
1114	error(30, temp);
1115	}
1116	ifp = create_FILE_BUFFER(inf, IFP);
1117	if(Lenstr(outf) <= 0) ofp = stdout;
1118	else if((ofp=fopen(outf, "w"))==NULL) {
1119	sprintf(temp, "Cannot open output file %s\n", outf);
1120	error(31, temp);
1121	}
1122	init();
1123	init_seq_data();
1124	init_genbank();
1125	init_embl();
1126
1127	#ifdef log
1128	fprintf(stderr, "Start converting...\n");
1129	#endif
1130
1131	while(embl_in(ifp)!=EOF) {
1132	data.numofseq++;
1133	if(etog()) genbank_out(ofp);
1134	else error(32,
1135	"Conversion from macke to genbank fails, Exit");
1136	init_genbank();
1137	init_embl();
1138	#ifdef log
1139	if((data.numofseq % 50)==0)
1140	fprintf(stderr, "%d sequences are converted...\n",
1141	data.numofseq);
1142	#endif
1143
1144	}
1145
1146	#ifdef log
1147	fprintf(stderr,
1148	"Total %d sequences have been processed\n", data.numofseq);
1149	#endif
1150	}
1151	/* -------------------------------------------------------------
1152	* Function etog()
1153	* Convert from embl to genbank format.
1154	*/
1155	int
1156	etog() {
1157
1158	int indi;
1159	char key[TOKENNUM], temp[LONGTEXT];
1160	char t1[TOKENNUM], t2[TOKENNUM], t3[TOKENNUM];
1161	/* char Dupstr(), genbank_date(); */
1162	/* void embl_key_word(), Cpystr(); */
1163	/* void etog_comments(), etog_reference(), Append_char(); */
1164	/* void replace_entry(); */
1165
1166	embl_key_word(data.embl.id, 0, key, TOKENNUM);
1167	if(Lenstr(data.embl.dr)>1) {
1168	/* get short_id from DR line if there is RDP def. */
1169	Cpystr(t3, "dummy");
1170	sscanf(data.embl.dr, "%s %s %s", t1, t2, t3);
1171	if(Cmpstr(t1, "RDP;")==EQ) {
1172	if(Cmpstr(t3, "dummy")!=EQ) {
1173	Cpystr(key, t3);
1174	} else Cpystr(key, t2);
1175	key[Lenstr(key)-1]='\0'; /* remove '.' */
1176	}
1177	}
1178	Cpystr(temp, key);
1179
1180	/* LOCUS */
1181	for(indi=Lenstr(temp); indi<13; temp[indi++]=' ') ;
1182	if(Lenstr(data.embl.dateu)>1) {
1183	sprintf((temp+10),
1184	"%7d bp RNA RNA %s\n",
1185	data.seq_length, genbank_date(data.embl.dateu));
1186	} else sprintf((temp+10),
1187	"7%d bp RNA RNA %s\n",
1188	data.seq_length, genbank_date(today_date()));
1189	replace_entry(&(data.gbk.locus), temp);
1190
1191	/* DEFINITION */
1192	if(Lenstr(data.embl.description)>1) {
1193
1194	replace_entry(&(data.gbk.definition),
1195	data.embl.description);
1196
1197	/* must have a period at the end */
1198	Append_char(&(data.gbk.definition), '.');
1199	}
1200
1201	/* SOURCE and DEFINITION if not yet defined */
1202	if(Lenstr(data.embl.os)>1) {
1203	replace_entry(&(data.gbk.source),
1204	data.embl.os);
1205
1206	replace_entry(&(data.gbk.organism),
1207	data.embl.os);
1208
1209	if(Lenstr(data.embl.description)<=1) {
1210	replace_entry(&(data.gbk.definition),
1211	data.embl.os);
1212	}
1213	}
1214
1215	/* COMMENT GenBank entry */
1216	if(Lenstr(data.embl.accession)>1)
1217	replace_entry(&(data.gbk.accession),
1218	data.embl.accession);
1219
1220	if(Lenstr(data.embl.keywords)>1&&data.embl.keywords[0]!='.')
1221	replace_entry(&(data.gbk.keywords),
1222	data.embl.keywords);
1223
1224	/* convert reference */
1225	etog_reference();
1226
1227	/* convert comments */
1228	etog_comments();
1229
1230	return(1);
1231	}
1232	/* ---------------------------------------------------------------------
1233	* Function etog_reference().
1234	* Convert reference from EMBL to GenBank format.
1235	*/
1236	void
1237	etog_reference() {
1238
1239	int indi, len, start, end;
1240	char temp[LONGTEXT];
1241	/* char etog_author(), etog_journal(); */
1242
1243	data.gbk.numofref = data.embl.numofref;
1244
1245	data.gbk.reference
1246	= (Reference)calloc(1,sizeof(Reference)data.embl.numofref);
1247
1248	for(indi=0; indi<data.embl.numofref; indi++) {
1249
1250	if(Lenstr(data.embl.reference[indi].processing)>1) {
1251	sscanf(data.embl.reference[indi].processing,
1252	"%d %d", &start, &end);
1253	end = -1; / will get negative from sscanf */
1254	sprintf(temp, "%d (bases %d to %d)\n", (indi+1), start, end);
1255	data.gbk.reference[indi].ref
1256	= (char*)Dupstr(temp);
1257	} else {
1258	sprintf(temp, "%d\n", (indi+1));
1259	data.gbk.reference[indi].ref = (char*)Dupstr(temp);
1260	}
1261
1262	if(Lenstr(data.embl.reference[indi].title)>1
1263	&&data.embl.reference[indi].title[0]!=';') {
1264
1265	/* remove '"' and ';', if there is any */
1266	len = Lenstr(data.embl.reference[indi].title);
1267	if(len>2&&data.embl.reference[indi].title[0]=='"'
1268	&&data.embl.reference[indi].title[len-2]==';'
1269	&&data.embl.reference[indi].title[len-3]=='"') {
1270	data.embl.reference[indi].title[len-3]='\n';
1271	data.embl.reference[indi].title[len-2]='\0';
1272	data.gbk.reference[indi].title = (char*)
1273	Dupstr(data.embl.reference[indi].title+1);
1274	data.embl.reference[indi].title[len-3]='"';
1275	data.embl.reference[indi].title[len-2]=';';
1276	} else data.gbk.reference[indi].title = (char*)
1277	Dupstr(data.embl.reference[indi].title);
1278
1279	} else data.gbk.reference[indi].title
1280	= (char*)Dupstr("\n");
1281
1282	/* GenBank AUTHOR */
1283	if(Lenstr(data.embl.reference[indi].author)>1)
1284
1285	data.gbk.reference[indi].author
1286	= etog_author(data.embl.reference[indi].author);
1287
1288	else data.gbk.reference[indi].author
1289	= (char*)Dupstr("\n");
1290
1291	if(Lenstr(data.embl.reference[indi].journal)>1)
1292
1293	data.gbk.reference[indi].journal
1294	= (char*)etog_journal(data.embl.reference[indi].journal);
1295
1296	else data.gbk.reference[indi].journal
1297	= (char*)Dupstr("\n");
1298
1299	data.gbk.reference[indi].standard
1300	= (char*)Dupstr("\n");
1301	}
1302	}
1303	/* -----------------------------------------------------------------
1304	* Function etog_author().
1305	* Convert EMBL author format to Genbank author format.
1306	*/
1307	char
1308	*etog_author(string)
1309	char *string;
1310	{
1311	int indi, /indj,/ indk, len, index;
1312	char token[TOKENNUM], *author;
1313	/* void Append(); */
1314
1315	author=(char*)Dupstr("");
1316	for(indi=index=0,len=Lenstr(string)-1; indi<len; indi++, index++) {
1317	if(string[indi]==','\|\|string[indi]==';') {
1318	token[index--]='\0';
1319	if(string[indi]==',') {
1320	if(Lenstr(author)>0) Append(&(author), ",");
1321	}
1322	else if(Lenstr(author)>0) {
1323	Append(&(author), " and");
1324	}
1325	/* search backward to find the first blank and replace the blank by ',' */
1326	for(indk=0; index>0&&indk==0; index--)
1327	if(token[index]==' ') {
1328	token[index]=',';
1329	indk=1;
1330	}
1331	Append(&(author), token);
1332	index = (-1);
1333	} else token[index]=string[indi];
1334	}
1335	Append(&(author), "\n");
1336	return(author);
1337	}
1338	/* ------------------------------------------------------------
1339	* Function etog_journal().
1340	* Convert jpurnal part from EMBL to GenBank format.
1341	*/
1342	char
1343	*etog_journal(string)
1344	char *string;
1345	{
1346	int indi, len, index;
1347	char journal, new_journal;
1348	char token[TOKENNUM];
1349	/* void Freespace(), Append(); */
1350
1351	sscanf(string, "%s", token);
1352	if(Cmpstr(token, "(in)")==EQ\|\|Cmpstr(token, "Submitted")==EQ
1353	\|\|Cmpstr(token, "Unpublished")==EQ) {
1354	/* remove '.' */
1355	string[Lenstr(string)-2]='\n';
1356	string[Lenstr(string)-1]='\0';
1357	new_journal = (char*)Dupstr(string);
1358	string[Lenstr(string)-1]='.';
1359	string[Lenstr(string)]='\n';
1360	return(new_journal);
1361	}
1362	journal=(char*)Dupstr(string);
1363	for(indi=0, len=Lenstr(journal); indi<len; indi++) {
1364	if(journal[indi]==':') {
1365	journal[indi]='\0';
1366	new_journal=(char*)Dupstr(journal);
1367	journal[indi]=':';
1368	Append(&new_journal, ", ");
1369	index=indi+1;
1370	}
1371	if(journal[indi]=='(') {
1372	journal[indi]='\0';
1373	Append(&new_journal, journal+index);
1374	Append(&new_journal, " ");
1375	journal[indi]='(';
1376	index=indi;
1377	}
1378	if(journal[indi]=='.') {
1379	journal[indi]='\0';
1380	Append(&new_journal, journal+index);
1381	journal[indi]='.';
1382	}
1383	}
1384	Freespace(&journal);
1385	Append(&new_journal, "\n");
1386	return(new_journal);
1387	}
1388	/* ---------------------------------------------------------------
1389	* Function etog_comments().
1390	* Convert comment part from EMBL to GenBank.
1391	*/
1392	void
1393	etog_comments() {
1394
1395	/* int Lenstr(); */
1396	/* void replace_entry(); */
1397	/* char Dupsstr(); /
1398
1399	/* RDP defined Organism Information comments */
1400	data.gbk.comments.orginf.exist = data.embl.comments.orginf.exist;
1401
1402	if(Lenstr(data.embl.comments.orginf.source)>1)
1403	replace_entry(&(data.gbk.comments.orginf.source),
1404	data.embl.comments.orginf.source);
1405
1406	if(Lenstr(data.embl.comments.orginf.cc)>1)
1407	replace_entry(&(data.gbk.comments.orginf.cc),
1408	data.embl.comments.orginf.cc);
1409
1410	if(Lenstr(data.embl.comments.orginf.formname)>1)
1411	replace_entry(&(data.gbk.comments.orginf.formname),
1412	data.embl.comments.orginf.formname);
1413
1414	if(Lenstr(data.embl.comments.orginf.nickname)>1)
1415	replace_entry(&(data.gbk.comments.orginf.nickname),
1416	data.embl.comments.orginf.nickname);
1417
1418	if(Lenstr(data.embl.comments.orginf.commname)>1)
1419	replace_entry(&(data.gbk.comments.orginf.commname),
1420	data.embl.comments.orginf.commname);
1421
1422	if(Lenstr(data.embl.comments.orginf.hostorg)>1)
1423	replace_entry(&(data.gbk.comments.orginf.hostorg),
1424	data.embl.comments.orginf.hostorg);
1425
1426	/* RDP defined Sequence Information comments */
1427	data.gbk.comments.seqinf.exist = data.embl.comments.seqinf.exist;
1428
1429	if(Lenstr(data.embl.comments.seqinf.RDPid)>1)
1430	replace_entry(&(data.gbk.comments.seqinf.RDPid),
1431	data.embl.comments.seqinf.RDPid);
1432
1433	if(Lenstr(data.embl.comments.seqinf.gbkentry)>1)
1434	replace_entry(&(data.gbk.comments.seqinf.gbkentry),
1435	data.embl.comments.seqinf.gbkentry);
1436
1437	if(Lenstr(data.embl.comments.seqinf.methods)>1)
1438	replace_entry(&(data.gbk.comments.seqinf.methods),
1439	data.embl.comments.seqinf.methods);
1440
1441	data.gbk.comments.seqinf.comp5 = data.embl.comments.seqinf.comp5;
1442
1443	data.gbk.comments.seqinf.comp3 = data.embl.comments.seqinf.comp3;
1444
1445	/* other comments */
1446	if(Lenstr(data.embl.comments.others)>1)
1447	replace_entry(&(data.gbk.comments.others),
1448	data.embl.comments.others);
1449	}
1450	/* ----------------------------------------------------------------
1451	* Function genbank_to_embl().
1452	* Convert from genbank to EMBL.
1453	*/
1454	void
1455	genbank_to_embl(inf, outf)
1456	char inf, outf;
1457	{
1458	FILE IFP, ofp;
1459	FILE_BUFFER ifp;
1460	char temp[TOKENNUM];
1461
1462	if((IFP=fopen(inf, "r"))==NULL) {
1463	sprintf(temp,
1464	"Cannot open input file %s, exit\n", inf);
1465	error(132, temp);
1466	}
1467	ifp = create_FILE_BUFFER(inf, IFP);
1468	if((ofp=fopen(outf, "w"))==NULL) {
1469	sprintf(temp,
1470	"Cannot open output file %s, exit\n", outf);
1471	error(133, temp);
1472	}
1473	init();
1474	init_genbank();
1475	init_embl();
1476	/* rewind(ifp); */
1477	while(genbank_in(ifp)!=EOF) {
1478	data.numofseq++;
1479	if(gtoe()) embl_out(ofp);
1480	init_genbank();
1481	init_embl();
1482	}
1483
1484	#ifdef log
1485	fprintf(stderr,
1486	"Total %d sequences have been processed\n",
1487	data.numofseq);
1488	#endif
1489
1490	destroy_FILE_BUFFER(ifp); fclose(ofp);
1491	}
1492	/* ------------------------------------------------------------
1493	* Function gtoe().
1494	* Genbank to EMBL.
1495	*/
1496	int
1497	gtoe() {
1498	/* void genbank_key_word(), replace_entry(); */
1499	/* void Cpystr(), Upper_case(); */
1500	/* void genbank_key_word(), Append(), Append_char(); */
1501	/* void gtoe_comments(), gtoe_reference(); */
1502	char token[TOKENNUM], temp[LONGTEXT], rdpid[TOKENNUM];
1503	/* char Dupstr(), today_date(), genbank_date(); /
1504	int indi /,length/;
1505
1506	genbank_key_word(data.gbk.locus, 0, token, TOKENNUM);
1507	Cpystr(temp, token);
1508	/* Adjust short-id, EMBL short_id always upper case */
1509	Upper_case(temp);
1510	if(Lenstr(token)>9) indi=9; else indi=Lenstr(token);
1511	for(; indi<10; indi++) temp[indi]=' ';
1512	sprintf(temp+10, "preliminary; RNA; UNA; %d BP.\n",
1513	data.seq_length);
1514	replace_entry(&(data.embl.id), temp);
1515
1516	/* accession number */
1517	if(Lenstr(data.gbk.accession)>1)
1518	/* take just the accession num, no version num. */
1519	replace_entry(&(data.embl.accession),
1520	data.gbk.accession);
1521
1522	/* date */
1523	if(Lenstr(data.gbk.locus)<61) {
1524	Cpystr(token, genbank_date(today_date()));
1525	} else {
1526	for(indi=0; indi<11; indi++)
1527	token[indi]=data.gbk.locus[indi+50];
1528	token[11]='\0';
1529	}
1530	sprintf(temp,
1531	"%s (Rel. 1, Last updated, Version 1)\n", token);
1532	replace_entry(&(data.embl.dateu), temp);
1533	sprintf(temp, "%s (Rel. 1, Created)\n", token);
1534	replace_entry(&(data.embl.datec), temp);
1535
1536	/* description */
1537	if(Lenstr(data.gbk.definition)>1)
1538	replace_entry(&(data.embl.description),
1539	data.gbk.definition);
1540
1541	/* EMBL KW line */
1542	if(Lenstr(data.gbk.keywords)>1) {
1543
1544	replace_entry(&(data.embl.keywords),
1545	data.gbk.keywords);
1546	Append_char(&(data.embl.keywords), '.');
1547
1548	} else replace_entry(&(data.embl.keywords), ".\n");
1549
1550	/* EMBL OS line */
1551	if(Lenstr(data.gbk.organism)>1)
1552	replace_entry(&(data.embl.os),
1553	data.gbk.organism);
1554
1555	/* reference */
1556	gtoe_reference();
1557
1558	/* EMBL DR line */
1559	sscanf(data.gbk.locus, "%s", token); /* short_id */
1560	if(Lenstr(data.gbk.comments.seqinf.RDPid)>1) {
1561	sscanf(data.gbk.comments.seqinf.RDPid, "%s", rdpid);
1562	sprintf(temp, "RDP; %s; %s.\n", rdpid, token);
1563	} else sprintf(temp, "RDP; %s.\n", token);
1564	replace_entry(&(data.embl.dr), temp);
1565
1566	gtoe_comments();
1567
1568	return(1);
1569	}
1570	/* ------------------------------------------------------------------
1571	* Function gtoe_reference().
1572	* Convert references from GenBank to EMBL.
1573	*/
1574	void
1575	gtoe_reference() {
1576
1577	int indi, start, end, refnum;
1578	char token[TOKENNUM];
1579	char t1[TOKENNUM], t2[TOKENNUM], t3[TOKENNUM];
1580	/* char gtoe_author(), gtoe_journal(); */
1581	/* void embl_verify_title(), Append_char(); */
1582
1583	data.embl.numofref=data.gbk.numofref;
1584
1585	if(data.gbk.numofref>0) {
1586	data.embl.reference = (Emblref*)malloc
1587	(sizeof(Emblref)*data.gbk.numofref);
1588	}
1589
1590	for(indi=0; indi<data.gbk.numofref; indi++) {
1591
1592	data.embl.reference[indi].title
1593	= (char*)Dupstr
1594	(data.gbk.reference[indi].title);
1595
1596	embl_verify_title(indi);
1597
1598	data.embl.reference[indi].journal
1599	= (char*)gtoe_journal
1600	(data.gbk.reference[indi].journal);
1601
1602	/* append a '.' if there is not any. */
1603	Append_char(&(data.embl.reference[indi].journal), '.');
1604
1605	data.embl.reference[indi].author
1606	= gtoe_author(data.gbk.reference[indi].author);
1607
1608	/* append a ';' if there is not any. */
1609	Append_char(&(data.embl.reference[indi].author), ';');
1610
1611	/* create processing information */
1612	start=end=0;
1613	if (data.gbk.reference[indi].ref) {
1614	sscanf(data.gbk.reference[indi].ref,
1615	"%d %s %d %s %d %s",
1616	&refnum, t1, &start, t2, &end, t3);
1617	}else{
1618	start = 0; end = 0;
1619	}
1620
1621	if(start!=0\|\|end!=0)
1622	{
1623	sprintf(token, "%d-%d\n",
1624	start, end);
1625	data.embl.reference[indi].processing
1626	= (char*)Dupstr(token);
1627	} else /* else change nothing about RP */
1628	data.embl.reference[indi].processing
1629	= (char*)Dupstr("\n");
1630
1631	} /* for each reference */
1632	}
1633	/* ----------------------------------------------------------------
1634	* Function gtoe_author().
1635	* Convert GenBank author to EMBL author.
1636	*/
1637	char
1638	*gtoe_author(author)
1639	char *author;
1640	{
1641	int indi, len, index, odd;
1642	char auth, string;
1643	/* void Append(), Freespace(); */
1644
1645	/* replace " and " by ", " */
1646	auth = (char*)Dupstr(author);
1647	if((index=find_pattern(auth, " and "))>0) {
1648	auth[index]='\0';
1649	string=(char*)Dupstr(auth);
1650	auth[index]=' '; /* remove '\0' for free space later */
1651	Append(&(string), ",");
1652	Append(&(string), auth+index+4);
1653	} else string=(char*)Dupstr(author);
1654
1655	for(indi=0,len=Lenstr(string), odd=1; indi<len; indi++) {
1656	if(string[indi]==',') {
1657	if (odd) {
1658	string[indi] = ' ';
1659	odd=0;
1660	}
1661	else {
1662	odd=1;
1663	}
1664	}
1665	}
1666
1667	Freespace(&auth);
1668	return(string);
1669
1670	}
1671	/* ------------------------------------------------------------
1672	* Function gtoe_journal().
1673	* Convert GenBank journal to EMBL journal.
1674	*/
1675	char
1676	*gtoe_journal(string)
1677	char *string;
1678	{
1679	char token[TOKENNUM], *journal;
1680	int indi, indj, index, len;
1681	/* void Append_char(); */
1682
1683	sscanf(string, "%s", token);
1684	if(Cmpstr(token, "(in)")==EQ\|\|Cmpstr(token, "Unpublished")==EQ
1685	\|\|Cmpstr(token, "Submitted")==EQ) {
1686	journal=(char*)Dupstr(string);
1687	Append_char(&journal, '.');
1688	return(journal);
1689	}
1690
1691	journal=(char*)Dupstr(string);
1692	for(indi=indj=index=0, len=Lenstr(journal); indi<len; indi++, indj++) {
1693	if(journal[indi]==',') {
1694	journal[indi]=':';
1695	indi++; /* skip blank after ',' */
1696	index=1;
1697	} else if(journal[indi]==' '&&index) {
1698	indj--;
1699	} else journal[indj]=journal[indi];
1700	}
1701
1702	journal[indj]='\0';
1703	Append_char(&journal, '.');
1704	return(journal);
1705	}
1706	/* ---------------------------------------------------------------
1707	* Function gtoe_comments().
1708	* Convert comment part from GenBank to EMBL.
1709	*/
1710	void
1711	gtoe_comments() {
1712	/* int Lenstr(); */
1713	/* void replace_entry(); */
1714	/* char Dupsstr(); /
1715
1716	/* RDP defined Organism Information comments */
1717	data.embl.comments.orginf.exist = data.gbk.comments.orginf.exist;
1718
1719	if(Lenstr(data.gbk.comments.orginf.source)>1)
1720	replace_entry(&(data.embl.comments.orginf.source),
1721	data.gbk.comments.orginf.source);
1722
1723	if(Lenstr(data.gbk.comments.orginf.cc)>1)
1724	replace_entry(&(data.embl.comments.orginf.cc),
1725	data.gbk.comments.orginf.cc);
1726
1727	if(Lenstr(data.gbk.comments.orginf.formname)>1)
1728	replace_entry(&(data.embl.comments.orginf.formname),
1729	data.gbk.comments.orginf.formname);
1730
1731	if(Lenstr(data.gbk.comments.orginf.nickname)>1)
1732	replace_entry(&(data.embl.comments.orginf.nickname),
1733	data.gbk.comments.orginf.nickname);
1734
1735	if(Lenstr(data.gbk.comments.orginf.commname)>1)
1736	replace_entry(&(data.embl.comments.orginf.commname),
1737	data.gbk.comments.orginf.commname);
1738
1739	if(Lenstr(data.gbk.comments.orginf.hostorg)>1)
1740	replace_entry(&(data.embl.comments.orginf.hostorg),
1741	data.gbk.comments.orginf.hostorg);
1742
1743	/* RDP defined Sequence Information comments */
1744	data.embl.comments.seqinf.exist = data.gbk.comments.seqinf.exist;
1745
1746	if(Lenstr(data.gbk.comments.seqinf.RDPid)>1)
1747	replace_entry(&(data.embl.comments.seqinf.RDPid),
1748	data.gbk.comments.seqinf.RDPid);
1749
1750	if(Lenstr(data.gbk.comments.seqinf.gbkentry)>1)
1751	replace_entry(&(data.embl.comments.seqinf.gbkentry),
1752	data.gbk.comments.seqinf.gbkentry);
1753
1754	if(Lenstr(data.gbk.comments.seqinf.methods)>1)
1755	replace_entry(&(data.embl.comments.seqinf.methods),
1756	data.gbk.comments.seqinf.methods);
1757
1758	data.embl.comments.seqinf.comp5 = data.gbk.comments.seqinf.comp5;
1759
1760	data.embl.comments.seqinf.comp3 = data.gbk.comments.seqinf.comp3;
1761
1762	/* other comments */
1763	if(Lenstr(data.gbk.comments.others)>1)
1764	replace_entry(&(data.embl.comments.others),
1765	data.gbk.comments.others);
1766	}
1767	/* ---------------------------------------------------------------
1768	* Function macke_to_embl().
1769	* Convert from macke to EMBL.
1770	*/
1771	void
1772	macke_to_embl(inf, outf)
1773	char inf, outf;
1774	{
1775	FILE IFP1, IFP2, IFP3, ofp;
1776	FILE_BUFFER ifp1, ifp2, ifp3;
1777	char temp[TOKENNUM];
1778
1779	if ((IFP1=fopen(inf, "r"))==NULL \|\|
1780	(IFP2=fopen(inf, "r"))==NULL \|\|
1781	(IFP3=fopen(inf, "r"))==NULL)
1782	{
1783	sprintf(temp, "Cannot open input file %s\n", inf);
1784	error(99, temp);
1785	}
1786
1787	ifp1 = create_FILE_BUFFER(inf, IFP1);
1788	ifp2 = create_FILE_BUFFER(inf, IFP2);
1789	ifp3 = create_FILE_BUFFER(inf, IFP3);
1790
1791	if(Lenstr(outf)<=0) ofp = stdout;
1792	else if((ofp=fopen(outf, "w"))==NULL) {
1793	sprintf(temp, "Cannot open output file %s\n", outf);
1794	error(43, temp);
1795	}
1796	init();
1797	init_seq_data();
1798	init_genbank();
1799	init_macke();
1800	init_embl();
1801
1802	#ifdef log
1803	fprintf(stderr, "Start converting...\n");
1804	#endif
1805
1806	while(macke_in(ifp1, ifp2, ifp3)!=EOF) {
1807
1808	data.numofseq++;
1809
1810	/* partial_mtoe() is particularly handling
1811	* subspecies information, not converting whole
1812	* macke format to embl */
1813
1814	if(mtog()&&gtoe()&&partial_mtoe()) embl_out(ofp);
1815	else error(14,
1816	"Conversion from macke to embl fails, Exit");
1817
1818	init_genbank();
1819	init_embl();
1820	init_macke();
1821
1822	#ifdef log
1823	if((data.numofseq % 50)==0)
1824	fprintf(stderr, "%d sequences are converted...\n",
1825	data.numofseq);
1826	#endif
1827
1828	}
1829
1830	#ifdef log
1831	fprintf(stderr,
1832	"Total %d sequences have been processed\n", data.numofseq);
1833	#endif
1834
1835	}
1836	/* --------------------------------------------------------------
1837	* Function partial_mtoe().
1838	* Handle subspecies information when converting from
1839	* Macke to EMBL.
1840	*/
1841	int partial_mtoe() {
1842
1843	int indj, indk;
1844	/* int not_ending_mark(); */
1845	/* void Freespace(), Append(), Append_rm_eoln(); */
1846
1847	if(Lenstr(data.macke.strain)>1) {
1848	if((indj=find_pattern(data.embl.comments.others, "*source:"))>=0 &&
1849	(indk=find_pattern (data.embl.comments.others+indj, "strain="))>=0)
1850	{
1851	; /* do nothing */
1852	}
1853	else {
1854	if(Lenstr(data.embl.comments.others)<=1) Freespace(&(data.embl.comments.others));
1855	Append(&(data.embl.comments.others), "*source: strain=");
1856	Append(&(data.embl.comments.others), data.macke.strain);
1857	if (not_ending_mark(data.embl.comments.others[Lenstr(data.embl.comments.others)-2])) {
1858	Append_rm_eoln (&(data.embl.comments.others), ";\n");
1859	}
1860	}
1861	}
1862
1863	if(Lenstr(data.macke.subspecies)>1) {
1864
1865	if((indj=find_pattern (data.embl.comments.others, "*source:"))>=0 &&
1866	((indk=find_pattern(data.embl.comments.others+indj, "subspecies="))>=0 \|\|
1867	(indk=find_pattern(data.embl.comments.others+indj, "sub-species="))>=0 \|\|
1868	(indk=find_pattern(data.embl.comments.others+indj, "subsp.="))>=0))
1869	{
1870	;/* do nothing */
1871	}
1872	else {
1873	if (Lenstr(data.embl.comments.others)<=1) Freespace (&(data.embl.comments.others));
1874
1875	Append(&(data.embl.comments.others), "*source: subspecies=");
1876	Append(&(data.embl.comments.others), data.macke.subspecies);
1877
1878	if (not_ending_mark(data.embl.comments.others[Lenstr(data.embl.comments.others)-2])) {
1879	Append_rm_eoln (&(data.embl.comments.others), ";\n");
1880	}
1881	}
1882	}
1883
1884	return(1);
1885	}

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