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feature_table.ift

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Last change on this file was 6092, checked in by westram, 15 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: 9.0 KB

Line
1	# This file is no complete import-filter.
2	# It is included from longgenbank.ift and longebi.ift
3	#
4	# includer has to
5	# set 't' to 'GB' or 'EBI' (used for tags)
6	# set 'u' to 'gb' or 'embl' (used as field name suffix)
7
8	IFNOTSET t "feature_table.ift expects SETGLOBAL 't'"
9	IFNOTSET u "feature_table.ift expects SETGLOBAL 'u'"
10
11	# for debugging purposes you may like to uncomment the next line (see also EOF)
12	# AUTOTAG "ft"
13
14	MATCH "FT source*"
15	SRT "source=*2: ="
16	# TAG "$t"
17	APPEND "nuc_region"
18
19	MATCH "FTx source mol_type"
20	SRT "mol_type=*2:\==:\"=:"
21	# TAG "$t"
22	APPEND "mol_type"
23
24	MATCH "FTx source citation"
25	SRT "citation=*2:\"=:\=="
26	# TAG "$t"
27	APPEND "biblio"
28
29	MATCH "FTx source cell_line"
30	SRT "cell_line=*2:\"=:\=="
31	# TAG "$t"
32	APPEND "cell_line"
33
34	MATCH "FTx source cell_type"
35	SRT "cell_type=*2:\"=:\=="
36	# TAG "$t"
37	APPEND "cell_type"
38
39	MATCH "FTx source clone"
40	SRT "clone=*2:\"=:\=="
41	# TAG "$t"
42	APPEND "clone"
43
44	MATCH "FTx source clone_lib"
45	SRT "clone_lib=*2:\"=:\=="
46	# TAG "$t"
47	APPEND "clone_lib"
48
49	MATCH "FTx source cultivar"
50	SRT "cultivar=*2:\"=:\=="
51	# TAG "$t"
52	APPEND "cultivar"
53
54	MATCH "FTx source db_xref="
55	SRT "db_xref=*2:\"=:\=="
56	TAG "$t"
57	APPEND "xref_1"
58
59	MATCH "FTx source db_xref="taxon"
60	SRT "db_xref=2:\:=2:\"=:\=="
61	# TAG "$t"
62	# APPEND "tax_xref_embl"
63	# APPEND "tax_xref_gb"
64	# set tax_xref_embl or tax_xref_gb (see definition in includer)
65	APPEND "tax_xref_$u"
66
67	MATCH "FTx source lab_host="
68	SRT "lab_host=*2:\"=:\=="
69	# TAG "$t"
70	APPEND "host"
71
72	MATCH "FTx source isolate="
73	SRT "isolate=*2:\"=:\=="
74	# TAG "$t"
75	APPEND "isolate"
76
77	MATCH "FTx source strain"
78	SRT "/strain=*2:\"=:\=="
79	# TAG "$t"
80	APPEND "strain"
81
82	MATCH "FTx source isolation_source"
83	SRT "/isolation_source=*2:\"=:\=="
84	# TAG "$t"
85	APPEND "isolation_source"
86
87	MATCH "FTx source country"
88	SRT "/country=*2:\"=:\=="
89	# TAG "$t"
90	APPEND "country"
91
92	MATCH "FTx source map"
93	SRT "/map=*2:\"=:\=="
94	# TAG "$t"
95	APPEND "map"
96
97	MATCH "FTx source lat_lon"
98	SRT "/lat_lon=*2:\"=:\=="
99	# TAG "$t"
100	APPEND "lat_lon"
101
102	MATCH "FTx source note"
103	SRT "/note=*2:\"=:\=="
104	TAG "$t"
105	APPEND "note"
106
107	MATCH "FTx source organelle"
108	SRT "/organelle=*2:\"=:\=="
109	# TAG "$t"
110	APPEND "organelle"
111
112	MATCH "FTx source plasmid"
113	SRT "/plasmid=*2:\"=:\=="
114	# TAG "$t"
115	APPEND "plasmid"
116
117	MATCH "FTx source serotype"
118	SRT "/serotype=*2:\"=:\=="
119	# TAG "$t"
120	APPEND "serotype"
121
122	MATCH "FTx source serovar"
123	SRT "/serovar=*2:\"=:\=="
124	# TAG "$t"
125	APPEND "serovar"
126
127	MATCH "FTx source sub_species"
128	SRT "/sub_species=*2:\"=:\=="
129	# TAG "$t"
130	APPEND "subspec"
131
132	MATCH "FTx source specimen_voucher"
133	SRT "/specimen_voucher=*2:\"=:\=="
134	# TAG "$t"
135	APPEND "specimen_voucher"
136
137	MATCH "FTx source specific_host"
138	SRT "/specific_host=*2:\"=:\=="
139	# TAG "$t"
140	APPEND "specific_host"
141
142	MATCH "FTx source tissue_type"
143	SRT "/tissue_type=*2:\"=:\=="
144	# TAG "$t"
145	APPEND "tissue"
146
147	MATCH "FTx source variety"
148	SRT "/variety=*2:\"=:\=="
149	# TAG "$t"
150	APPEND "variety"
151
152	MATCH "FTx source collected_by"
153	SRT "/collected_by=*2:\"=:\=="
154	# TAG "$t"
155	APPEND "collected_by"
156
157	MATCH "FTx source collection_date"
158	SRT "/collection_date=*2:\"=:\=="
159	# TAG "$t"
160	APPEND "collection_date"
161
162	MATCH "FT CDS*"
163	SRT "<=:>=:CDS..=2: ="
164	WRITE_INT "start"
165
166	MATCH "FT CDS*"
167	SRT "<=:>=:CDS..=3: ="
168	WRITE_INT "stop"
169
170	MATCH "FT CDS*"
171	SRT "<=:>=:CDS=*2: ="
172	SETVAR z
173	IFNOTSET z "No CDS location seen"
174	# TAG "$t"
175	APPEND "cds_position"
176
177	MATCH "FTx CDS allele"
178	SRT "allele=*2:\"=:\=="
179	# TAG "$t"
180	APPEND "allele"
181
182	MATCH "FTx CDS citation"
183	SRT "citation=*2:\"=:\=="
184	# TAG "$t"
185	APPEND "citation"
186
187	MATCH "FTx CDS codon_start"
188	SRT "codon_start=*2:\"=:\=="
189	# TAG "$t"
190	APPEND "codon_start"
191
192	MATCH "FTx CDS db_xref"
193	SRT "db_xref=*2:\"=:\=="
194	TAG "$t"
195	APPEND "xref_2"
196
197	MATCH "FTx CDS function"
198	SRT "function=*2:\"=:\=="
199	# TAG "$t"
200	APPEND "function"
201
202	MATCH "FTx CDS EC_number"
203	SRT "EC_number=*2:\"=:\=="
204	# TAG "$t"
205	APPEND "ec_number"
206
207	MATCH "FTx CDS transl_table"
208	SRT "transl_table=*2:\"=:\=="
209	# TAG "$t"
210	APPEND "transl_table"
211
212	MATCH "FTx CDS gene"
213	SRT "gene=*2:\"=:\=="
214	# TAG "$t"
215	APPEND "gene"
216
217	MATCH "FTx CDS product"
218	SRT "product=*2:\"=:\=="
219	# TAG "$t"
220	APPEND "product"
221
222	MATCH "FTx CDS operon"
223	SRT "operon=*2:\"=:\=="
224	# TAG "$t"
225	APPEND "operon"
226
227	MATCH "FTx CDS protein_id"
228	SRT "protein_id=*2:\"=:\=="
229	# TAG "$t"
230	APPEND "protein_id"
231
232	#MATCH "FTx CDS translation"
233	# SRT "translation=*2:\"=:\=="
234	# TAG "$t"
235	# APPEND "translation"
236
237	MATCH "FT rRNA*"
238	SRT "rRNA=2: =:..=1:<=:>="
239	WRITE_INT "start"
240
241	MATCH "FT rRNA *"
242	SRT "rRNA=2: =:..=2:<=:>="
243	WRITE_INT "stop"
244
245	MATCH "FTx rRNA gene"
246	SRT "gene=*2:\==:"="
247	# TAG "$t"
248	APPEND "gene"
249
250	MATCH "FTx rRNA product"
251	SRT "product=*2:\==:"="
252	# TAG "$t"
253	APPEND "product"
254
255	#MATCH "FT *"
256	# SRT "FT ="
257	# APPEND "ebi_comment"
258
259	# AUTOTAG

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