/
genbank_silva.ift
141 lines (106 loc) · 4.14 KB
/
genbank_silva.ift
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
#Modified by FOG, 17.05.2009#
#type INT for start, stop and insdc added#
#some changes to fields#
AUTODETECT "LOCUS *\nORIGIN*"
#Global settings:
KEYWIDTH 12
FILETAG GB
BEGIN "LOCUS*"
MATCH "LOCUS *"
SRT "* *=*1"
WRITE "name"
MATCH "LOCUS *"
SRT "* *=*1"
WRITE "id"
MATCH "ACCESSION *"
ACI "extract_words("0123456789",4.0)"
WRITE "acc"
MATCH "PROJECT"
WRITE_INT "insdc"
MATCH "LOCUS *"
SRT " = : = : = : = :* * * * * * *=*7"
WRITE "date"
MATCH "DEFINITION"
TAG "GB"
WRITE "description"
MATCH " ORGANISM *"
SRT "* * *=*1 *2:*|*=*1"
WRITE "full_name"
MATCH " ORGANISM *|*"
SRT "*|*=*2"
TAG "GB"
WRITE "tax_embl"
MATCH " ORGANISM *"
SRT "* * *=*1 *2:*|*=*1"
TAG "GB"
WRITE "tax_embl_name"
MATCH "REFERENCE *(bases*"
SRT "*(*=*2:bases=:to=-: =:)="
APPEND "nuc_rp"
MATCH " PUBMED *"
APPEND "pubmed_id"
MATCH " AUTHORS *"
APPEND "author"
MATCH " TITLE *"
APPEND "title"
MATCH " JOURNAL *"
APPEND "journal"
MATCH " JOURNAL *Submitted*"
SRT "*Submitted*=*2:\(*\)*=*1"
WRITE "submit_date"
MATCH " source*"
SRT "*source*=*2: =:*|*=*1"
WRITE "nuc_region"
MATCH "*/clone*"
SRT "*clone*=*2:\"=:\==:*|*=*1"
APPEND "clone"
MATCH "*/db_xref="taxon*"
SRT "*db_xref*=*2:*\:*=*2:\"=:\==:*|*=*1"
TAG "GB"
APPEND "tax_xref_embl"
MATCH "*/isolate=*"
SRT "*isolate*=*2:\"=:\==:*|*=*1"
APPEND "isolate"
MATCH "*/strain*"
SRT "*/strain*=*2:\"=:\==:*|*=*1"
APPEND "strain"
MATCH "*/isolation_source*"
SRT "*/isolation_source*=*2:\"=:\==:*|*=*1"
APPEND "isolation_source"
MATCH "*/country*"
SRT "*/country*=*2:\"=:\==:*|*=*1"
APPEND "country"
MATCH "*/lat_lon*"
SRT "*/lat_lon*=*2:\"=:\==:*|*=*1"
APPEND "lat_lon"
MATCH "*/specimen_voucher*"
SRT "*/specimen_voucher*=*2:\"=:\==:*|*=*1"
APPEND "specimen_voucher"
MATCH "*/specific_host*"
SRT "*/specific_host*=*2:\"=:\==:*|*=*1"
APPEND "specific_host"
MATCH "*/collected_by*"
SRT "*/collected_by*=*2:\"=:\==:*|*=*1"
APPEND "collected_by"
MATCH "*/collection_date*"
SRT "*/collection_date*=*2:\"=:\==:*|*=*1"
APPEND "collection_date"
MATCH " rRNA*"
SRT "*..*=*1:<=:>="
WRITE_INT "start"
MATCH " rRNA *"
SRT "*..*=*2:<=:>=:*|*=*1"
WRITE_INT "stop"
MATCH " rRNA*/gene*"
SRT "*gene*=*2:\==:"=:*|*=*1"
APPEND "gene"
MATCH " rRNA*/product*"
SRT "*product*=*2:\==:"=:*|*=*1"
APPEND "product"
SEQUENCEAFTER "ORIGIN*"
SEQUENCESRT " =:~=.:*Check*..="
SEQUENCEACI "remove("0123456789 /")"
SEQUENCECOLUMN 0
SEQUENCEEND "//"
CREATE_ACC_FROM_SEQUENCE
END "//"