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genbank_silva.ift
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genbank_silva.ift
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#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 "//"