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Last change on this file was 6092, checked in by westram, 16 years ago
import filters mostly SILVA compatible (thx to Frank Oliver) moved feature- into separate filter which is included by longebi.ift and longgenbank.ift added AUTOTAGging (commented out)
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 8.6 KB

Line
1	# Modified by FOG 27.06.2009
2	# start, stop added
3	# type INT for start, stop added
4	# acc parsing changed
5	# a lot of stuff removed
6	# IFNOTSET added
7
8	AUTODETECT "LOCUS s\nORIGIN"
9	KEYWIDTH 12
10	FILETAG RDP
11
12	BEGIN "LOCUS*"
13
14	MATCH "LOCUS *"
15	SRT "* =1"
16	WRITE "name"
17
18	MATCH "LOCUS *"
19	SRT "* =1"
20	TAG "RDP"
21	WRITE "id"
22
23	#MATCH "LOCUS *"
24	# SRT " = : = : = : = :* * =2"
25	# TAG "RDP"
26	# WRITE "db_nuc"
27
28	MATCH "LOCUS *"
29	SRT " = : = : = : = :* * * * * * =7"
30	TAG "RDP"
31	WRITE "date"
32
33	MATCH "DEFINITION *"
34	TAG "RDP"
35	WRITE "description"
36
37	MATCH "COMMENTGenbank"
38	SRT "Genbank\: =2:\|=:(*=:;=:not submitted="
39	ACI "extract_words("0123456789",4.0)"
40	WRITE "acc"
41
42	#MATCH "COMMENTGenbank"
43	# SRT "Genbank\: =2:\|=:(*=:;=:not submitted="
44	# ACI "extract_words("0123456789",4.0)"
45	# WRITE "db_acc"
46
47	#MATCH "VERSION *"
48	# TAG "RDP"
49	# WRITE "version"
50
51	MATCH "KEYWORDS"
52	# TAG "RDP"
53	WRITE "keywd_RDP"
54
55	#MATCH "SOURCE *"
56	# TAG "RDP"
57	# WRITE "source"
58
59	MATCH " ORGANISM *"
60	# TAG "RDP"
61	SRT "\|=*1"
62	WRITE "tax_rdp_name"
63
64	MATCH " ORGANISM *"
65	# TAG "RDP"
66	SRT "\|=*2"
67	WRITE "tax_rdp"
68
69	MATCH " ORGANISM *"
70	SRT "* * =1 2:\|=1"
71	WRITE "full_name"
72
73	MATCH "REFERENCE *"
74	SRT "* =1"
75	SETVAR x
76	IFNOTSET x "No REFERENCE entry seen"
77	# TAG "RDP"
78	# APPEND "num_bib"
79
80	MATCH "REFERENCE *"
81	SRT "(=:)=:?=(?)"
82	# TAG "RDP"
83	APPEND "nuc_rp"
84
85	MATCH " AUTHORS *"
86	SRT "=($x)\: "
87	# TAG "RDP"
88	APPEND "author"
89
90	MATCH " TITLE *"
91	SRT "=($x)\: "
92	# TAG "RDP"
93	APPEND "title"
94
95	MATCH " JOURNAL *"
96	SRT "=($x)\: "
97	# TAG "RDP"
98	APPEND "journal"
99
100	#MATCH " MEDLINE *"
101	# SRT "=($x)\: "
102	# TAG "RDP"
103	# APPEND "medline_id"
104
105	MATCH " sourcecell_line"
106	SRT "/cell_line\=\"\"=2"
107	TAG "RDP"
108	WRITE "cell_line"
109
110	MATCH " sourcecell_type"
111	SRT "/cell_type\=\"\"=2"
112	TAG "RDP"
113	WRITE "cell_type
114
115	MATCH " sourcecultivar"
116	SRT "/cultivar\=\"\"=2"
117	TAG "RDP"
118	WRITE "cultivar"
119
120	MATCH " sourcedb_xref"
121	SRT "/db_xref\=\"\"=2"
122	TAG "RDP"
123	WRITE "tax_xref_embl"
124
125	MATCH " sourceisolate"
126	SRT "/isolate\=\"\"=2"
127	TAG "RDP"
128	WRITE "isolate"
129
130	MATCH " sourceisolation_source"
131	SRT "/isolation_source\=\"\"=2"
132	TAG "RDP"
133	WRITE "isolation_source"
134
135	MATCH " sourceclone"
136	SRT "/clone\=\"\"=2"
137	TAG "RDP"
138	WRITE "clone"
139
140	MATCH " sourcemap"
141	SRT "/map\=\"\"=2"
142	TAG "RDP"
143	WRITE "map"
144
145	MATCH " sourceorganelle"
146	SRT "/organelle\=\"\"=2"
147	TAG "RDP"
148	WRITE "organelle"
149
150	MATCH " sourceplasmid"
151	SRT "/plasmid\=\"\"=2"
152	TAG "RDP"
153	WRITE "plasmid"
154
155	MATCH " sourcesero_type"
156	SRT "/sero_type\=\"\"=2"
157	TAG "RDP"
158	WRITE "serotype"
159
160	MATCH " sourcesero_var"
161	SRT "/sero_var\=\"\"=2"
162	TAG "RDP"
163	WRITE "serovar"
164
165	MATCH " sourcespecimen_voucher"
166	SRT "/specimen_voucher\=\"\"=2"
167	TAG "RDP"
168	WRITE "voucher"
169
170	MATCH " sourcespecific_host"
171	SRT "/specific_host\=\"\"=2"
172	TAG "RDP"
173	WRITE "host"
174
175	MATCH " sourcestrain="
176	# TAG "RDP"
177	SRT "strain\=\"\"=2"
178	WRITE "strain"
179
180	MATCH " sourcesub_species="
181	TAG "RDP"
182	SRT "sub_species\=\"\"=2"
183	WRITE "subspec"
184
185	MATCH " sourcesub_strain="
186	TAG "RDP"
187	SRT "sub_strain\=\"\"=2"
188	WRITE "substrain"
189
190	MATCH " sourcetissue_type="
191	TAG "RDP"
192	SRT "tissue_type\=\"\"=2"
193	WRITE "tissue"
194
195	MATCH " sourcenote"
196	SRT "/note\=\"\"=2"
197	TAG "RDP"
198	WRITE "note"
199
200	MATCH " rRNAdb_xref"
201	SRT "/db_xref\=\"\"=2"
202	TAG "RDP"
203	APPEND "tax_xref_embl"
204
205	MATCH " rRNAevidence"
206	SRT "/evidence\=\"\"=2"
207	TAG "RDP"
208	APPEND "evidence"
209
210	MATCH " rRNAallele"
211	SRT "/allele\=\"\"=2"
212	TAG "RDP"
213	APPEND "allele"
214
215	MATCH " rRNAfunction"
216	SRT "/function\=\"\"=2"
217	TAG "RDP"
218	APPEND "function"
219
220	MATCH " rRNAcitation"
221	SRT "/citation\=\"\"=2"
222	TAG "RDP"
223	APPEND "citation"
224
225	MATCH " rRNAgene"
226	SRT "/gene\=\"\"=2"
227	TAG "RDP"
228	APPEND "gene"
229
230	MATCH " rRNAmap"
231	SRT "/map\=\"\"=2"
232	TAG "RDP"
233	APPEND "map"
234
235	MATCH " rRNAnote"
236	SRT "/note\=\"\"=2"
237	TAG "RDP"
238	APPEND "note"
239
240	MATCH " rRNAoperon"
241	SRT "/operon\=\"\"=2"
242	TAG "RDP"
243	APPEND "operon"
244
245	MATCH " rRNAproduct"
246	SRT "/product\=\"\"=2"
247	TAG "RDP"
248	APPEND "product"
249
250	MATCH " rRNA*"
251	SRT "..=*1:<=:>="
252	WRITE_INT "start"
253
254	MATCH " rRNA *"
255	SRT "..=2:<=:>=:\|=1"
256	WRITE_INT "stop"
257
258	SEQUENCEAFTER "ORIGIN*"
259	SEQUENCESRT " =:~=.:Check..="
260	SEQUENCEACI "remove("0123456789 /")"
261	SEQUENCECOLUMN 0
262	SEQUENCEEND "//"
263	CREATE_ACC_FROM_SEQUENCE
264
265	END "//"

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