|
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:
5.6 KB
|
| Line | |
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| 1 | # Modified by FOG, 27.06.2009 |
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| 2 | # mostly synchronized with ebi_silva |
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| 3 | |
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| 4 | KEYWIDTH 5 |
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| 5 | FILETAG "EBI" |
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| 6 | |
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| 7 | BEGIN "ID*" |
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| 8 | |
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| 9 | # set variables used by feature table |
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| 10 | SETGLOBAL t EBI |
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| 11 | SETGLOBAL u embl |
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| 12 | |
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| 13 | # uncomment next line to tag ALL fields with [EBI] |
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| 14 | # AUTOTAG "EBI" |
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| 15 | |
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| 16 | |
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| 17 | MATCH "ID *" |
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| 18 | SRT "* *=*1" |
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| 19 | WRITE "name" |
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| 20 | |
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| 21 | MATCH "ID *" |
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| 22 | SRT "*;*=*1" |
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| 23 | TAG "EBI" |
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| 24 | WRITE "id" |
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| 25 | |
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| 26 | MATCH "ID *" |
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| 27 | SRT "*; SV *;*=*2" |
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| 28 | WRITE_INT "version" |
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| 29 | |
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| 30 | #MATCH "ID *" |
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| 31 | # SRT "*;*;*;*;*;*;* * BP.=*8" |
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| 32 | # TAG "EBI" |
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| 33 | # WRITE "db_nuc" |
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| 34 | |
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| 35 | MATCH "AC *" |
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| 36 | ACI "extract_words("0123456789",2.0)" |
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| 37 | WRITE "acc" |
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| 38 | |
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| 39 | #MATCH "AC *" |
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| 40 | # TAG "EBI" |
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| 41 | # ACI "extract_words("0123456789",4.0)" |
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| 42 | # WRITE "db_acc" |
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| 43 | |
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| 44 | MATCH "PR *" |
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| 45 | SRT "PR *=*:*\:*=*2:;=" |
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| 46 | WRITE_INT "insdc" |
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| 47 | |
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| 48 | MATCH "DT *Created*" |
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| 49 | SRT "DT *=*:* \(*=*1;" |
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| 50 | # TAG "EBI" |
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| 51 | APPEND "date" |
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| 52 | |
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| 53 | MATCH "DT *updated*" |
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| 54 | SRT "DT *=*:* \(*=*1" |
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| 55 | # TAG "EBI" |
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| 56 | APPEND "date" |
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| 57 | |
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| 58 | MATCH "DE *" |
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| 59 | SRT "DE *=*:;=" |
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| 60 | # TAG "EBI" |
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| 61 | APPEND "description" |
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| 62 | |
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| 63 | MATCH "KW *" |
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| 64 | SRT "KW *=*" |
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| 65 | # TAG "EBI" |
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| 66 | APPEND "keywords" |
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| 67 | |
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| 68 | MATCH "OS *" |
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| 69 | SRT "OS *=*:* * *=*1 *2" |
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| 70 | WRITE "full_name" |
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| 71 | |
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| 72 | MATCH "OS *" |
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| 73 | SRT "OS *=*" |
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| 74 | TAG "EBI" |
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| 75 | WRITE "db_name" |
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| 76 | |
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| 77 | MATCH "OS *." |
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| 78 | SRT "OS *=*:.=" |
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| 79 | WRITE "tax_embl_name" |
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| 80 | |
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| 81 | #MATCH "OC *" |
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| 82 | # SRT "OC *=*" |
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| 83 | # TAG "EBI" |
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| 84 | # APPEND "tax" |
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| 85 | |
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| 86 | MATCH "OC *" |
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| 87 | SRT "OC *=*" |
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| 88 | APPEND "tax_embl" |
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| 89 | |
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| 90 | MATCH "OG *" |
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| 91 | SRT "OG *=*" |
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| 92 | # TAG "EBI" |
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| 93 | APPEND "organelle" |
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| 94 | |
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| 95 | MATCH "RN *" |
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| 96 | SRT "RN *=*:[=:]=" |
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| 97 | SETVAR x |
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| 98 | IFNOTSET x "No RN entry seen" |
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| 99 | # TAG "EBI" |
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| 100 | # APPEND "num_bib" |
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| 101 | |
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| 102 | MATCH "RP *" |
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| 103 | SRT "RP *=*:*=[$x]\: *" |
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| 104 | # TAG "EBI" |
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| 105 | APPEND "nuc_rp" |
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| 106 | |
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| 107 | MATCH "RC *" |
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| 108 | SRT "RC *=*:*=[$x]\: *" |
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| 109 | TAG "EBI" |
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| 110 | APPEND "author_com_1" |
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| 111 | |
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| 112 | MATCH "RX MEDLINE*" |
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| 113 | SRT "*MEDLINE*=*2:;=: =:.=" |
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| 114 | # SRT "*MEDLINE*=*2:;=: =:.=:*=[$x]\: *" |
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| 115 | TAG "EBI" |
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| 116 | APPEND "medline_id" |
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| 117 | |
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| 118 | MATCH "RX DOI*" |
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| 119 | SRT "*DOI*=*2:;=: =:.=" |
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| 120 | # SRT "*DOI*=*2:;=: =:*=[$x]\: *" |
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| 121 | # TAG "EBI" |
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| 122 | APPEND "publication_doi" |
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| 123 | |
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| 124 | MATCH "RX PUBMED*" |
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| 125 | SRT "*PUBMED*=*2:;=: =:.=" |
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| 126 | # SRT "*PUBMED*=*2:;=: =:.=:*=[$x]\: *" |
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| 127 | # TAG "EBI" |
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| 128 | APPEND "pubmed_id" |
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| 129 | |
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| 130 | MATCH "RG *" |
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| 131 | SRT "RG *=*:*=[$x]\: *" |
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| 132 | TAG "EBI" |
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| 133 | APPEND "refgrp" |
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| 134 | |
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| 135 | MATCH "RA *" |
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| 136 | SRT "RA *=*:;=:*=[$x]\: *" |
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| 137 | # TAG "EBI" |
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| 138 | APPEND "author" |
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| 139 | |
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| 140 | MATCH "RT *" |
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| 141 | SRT "RT *=*:;=:"=:*=[$x]\: *" |
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| 142 | # TAG "EBI" |
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| 143 | APPEND "title" |
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| 144 | |
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| 145 | MATCH "RL *)." |
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| 146 | SRT "RL *=*:*=[$x]\: *" |
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| 147 | # TAG "EBI" |
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| 148 | APPEND "journal" |
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| 149 | |
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| 150 | MATCH "RL *Submitted*" |
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| 151 | SRT "RL *=*:Submitted=:\(*\)*=*1" |
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| 152 | # TAG "EBI" |
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| 153 | WRITE "submit_date" |
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| 154 | |
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| 155 | MATCH "RL *" |
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| 156 | SRT "*Submitted*bases.=:*.\n*=*2" |
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| 157 | # TAG "EBI" |
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| 158 | APPEND "submit_author" |
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| 159 | |
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| 160 | MATCH "RL (er)*" |
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| 161 | SRT "RL (er)*=*" |
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| 162 | # TAG "EBI" |
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| 163 | APPEND "e_pub" |
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| 164 | |
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| 165 | MATCH "DR *" |
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| 166 | SRT "DR *; *=*1\: *2:;=" |
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| 167 | TAG "EBI" |
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| 168 | APPEND "ref_1" |
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| 169 | |
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| 170 | MATCH "CC *" |
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| 171 | SRT "CC *=*" |
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| 172 | TAG "EBI" |
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| 173 | APPEND "author_com_2" |
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| 174 | |
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| 175 | # ----------------------------------------------------------------- |
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| 176 | # Feature table (used by longebi.ift and longgenbank.ift!) |
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| 177 | |
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| 178 | INCLUDE "feature_table.ift" |
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| 179 | |
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| 180 | # --------------------------------------------------------------- |
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| 181 | |
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| 182 | SEQUENCEAFTER "SQ*" |
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| 183 | SEQUENCESRT "*Check*..*=*3" |
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| 184 | SEQUENCEACI "remove("0123456789 /")" |
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| 185 | SEQUENCEEND "//" |
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| 186 | |
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| 187 | CREATE_ACC_FROM_SEQUENCE |
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| 188 | |
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| 189 | END "//" |
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