| 1 | #Modified by FOG, 17.05.2009# |
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| 2 | #field type INT added for start, stop, insdc, version# |
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| 3 | |
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| 4 | AUTODETECT "ID *\nFT rRNA *\nSQ*" |
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| 5 | # Global settings: |
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| 6 | KEYWIDTH 5 |
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| 7 | FILETAG "EBI" |
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| 8 | |
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| 9 | BEGIN "ID*" |
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| 10 | |
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| 11 | MATCH "ID *" |
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| 12 | SRT "* *=*1" |
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| 13 | WRITE "name" |
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| 14 | |
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| 15 | MATCH "ID *" |
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| 16 | SRT "*; SV *;*=*2" |
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| 17 | WRITE_INT "version" |
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| 18 | |
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| 19 | MATCH "AC *" |
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| 20 | ACI "extract_words("0123456789",4.0)" |
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| 21 | WRITE "acc" |
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| 22 | |
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| 23 | MATCH "PR *" |
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| 24 | SRT "PR *=*:*\:*=*2:;=" |
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| 25 | WRITE_INT "insdc" |
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| 26 | |
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| 27 | MATCH "DT *Created*" |
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| 28 | SRT "DT *=*:* \(*=*1;" |
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| 29 | APPEND "date" |
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| 30 | |
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| 31 | MATCH "DT *updated*" |
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| 32 | SRT "DT *=*:* \(*=*1:" |
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| 33 | APPEND "date" |
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| 34 | |
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| 35 | MATCH "DE *" |
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| 36 | SRT "DE *=*:;=" |
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| 37 | APPEND "description" |
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| 38 | |
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| 39 | MATCH "OS *" |
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| 40 | SRT "OS *=*" |
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| 41 | WRITE "full_name" |
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| 42 | |
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| 43 | MATCH "OC *" |
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| 44 | SRT "OC *=*" |
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| 45 | APPEND "tax_embl" |
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| 46 | |
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| 47 | MATCH "OS *" |
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| 48 | SRT "OS *=*" |
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| 49 | WRITE "tax_embl_name" |
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| 50 | |
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| 51 | MATCH "RP *" |
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| 52 | SRT "RP *=*" |
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| 53 | APPEND "nuc_rp" |
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| 54 | |
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| 55 | MATCH "RX DOI*" |
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| 56 | SRT "*DOI*=*2:;=: =" |
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| 57 | WRITE "publication_doi" |
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| 58 | |
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| 59 | MATCH "RX PUBMED*" |
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| 60 | SRT "*PUBMED*=*2:;=: =:.=" |
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| 61 | WRITE "pubmed_id" |
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| 62 | |
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| 63 | MATCH "RA *" |
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| 64 | SRT "RA *=*:;=" |
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| 65 | APPEND "author" |
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| 66 | |
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| 67 | MATCH "RT *" |
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| 68 | SRT "RT *=*:;=:"=" |
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| 69 | APPEND "title" |
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| 70 | |
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| 71 | MATCH "RL *)." |
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| 72 | SRT "RL *=*:\).=)" |
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| 73 | APPEND "journal" |
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| 74 | |
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| 75 | MATCH "RL *Submitted*" |
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| 76 | SRT "RL *=*:Submitted=:\(*\)*=*1" |
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| 77 | WRITE "submit_date" |
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| 78 | |
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| 79 | MATCH "RL *" |
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| 80 | SRT "*Submitted*bases.=:*.\n*=*2" |
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| 81 | APPEND "submit_author" |
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| 82 | |
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| 83 | MATCH "FT source*" |
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| 84 | SRT "*source*=*2: =" |
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| 85 | WRITE "nuc_region" |
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| 86 | |
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| 87 | MATCH "FT *clone*" |
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| 88 | SRT "*clone*=*2:\"=:\==" |
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| 89 | APPEND "clone" |
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| 90 | |
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| 91 | MATCH "FT *db_xref=*taxon*" |
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| 92 | SRT "*db_xref*=*2:*\:*=*2:\"=:\==" |
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| 93 | APPEND "tax_xref_embl" |
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| 94 | |
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| 95 | MATCH "FT *isolate=*" |
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| 96 | SRT "*isolate*=*2:\"=:\==" |
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| 97 | APPEND "isolate" |
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| 98 | |
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| 99 | MATCH "FT *strain*" |
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| 100 | SRT "*/strain*=*2:\"=:\==" |
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| 101 | APPEND "strain" |
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| 102 | |
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| 103 | MATCH "FT *isolation_source*" |
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| 104 | SRT "*/isolation_source*=*2:\"=:\==" |
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| 105 | APPEND "isolation_source" |
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| 106 | |
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| 107 | MATCH "FT *country*" |
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| 108 | SRT "*/country*=*2:\"=:\==" |
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| 109 | APPEND "country" |
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| 110 | |
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| 111 | MATCH "FT *lat_lon*" |
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| 112 | SRT "*/lat_lon*=*2:\"=:\==" |
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| 113 | APPEND "lat_lon" |
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| 114 | |
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| 115 | MATCH "FT *specimen_voucher*" |
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| 116 | SRT "*/specimen_voucher*=*2:\"=:\==" |
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| 117 | APPEND "specimen_voucher" |
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| 118 | |
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| 119 | MATCH "FT *specific_host*" |
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| 120 | SRT "*/specific_host*=*2:\"=:\==" |
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| 121 | APPEND "specific_host" |
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| 122 | |
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| 123 | MATCH "FT *collected_by*" |
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| 124 | SRT "*/collected_by*=*2:\"=:\==" |
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| 125 | APPEND "collected_by" |
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| 126 | |
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| 127 | MATCH "FT *collection_date*" |
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| 128 | SRT "*/collection_date*=*2:\"=:\==" |
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| 129 | APPEND "collection_date" |
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| 130 | |
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| 131 | MATCH "FT rRNA*" |
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| 132 | SRT "*rRNA*=*2: =:*..*=*1:<=:>=" |
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| 133 | |
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| 134 | WRITE_INT "start" |
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| 135 | |
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| 136 | MATCH "FT rRNA *" |
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| 137 | SRT "*rRNA*=*2: =:*..*=*2:<=:>=" |
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| 138 | WRITE_INT "stop" |
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| 139 | |
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| 140 | MATCH "FT *gene*" |
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| 141 | SRT "*gene*=*2:\==:"=" |
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| 142 | APPEND "gene" |
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| 143 | |
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| 144 | MATCH "FT *product*" |
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| 145 | SRT "*product*=*2:\==:"=" |
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| 146 | APPEND "product" |
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| 147 | |
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| 148 | SEQUENCEAFTER "SQ*" |
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| 149 | SEQUENCESRT "*Check*..*=*3" |
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| 150 | SEQUENCEACI "remove("0123456789 /")" |
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| 151 | SEQUENCEEND "//" |
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| 152 | CREATE_ACC_FROM_SEQUENCE |
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| 153 | # DONT_GEN_NAMES |
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| 154 | |
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| 155 | END "//" |
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