source: branches/profile/lib/import/older/fasta_contextual_data_1_03.ift

# written by Renzo Kottmann rkottman@mpi-bremen.de 2008-08
# modified by Joerg Peplies, Frank Oliver Gloeckner
# start field is instantly set to 1
# Version 1.03 last modified 2008-11-01
# work out solution for PCR_primers
# fasta identifier (">*") goes now to field "fasta_id" (new!)
# content of contextual data field "organism" goes to ARB field "full_name"

#AUTODETECT "*[*"
KEYWIDTH 1

BEGIN   ">??*"

MATCH   ">*"
        SRT "* *=*1:*\t*=*1"
        WRITE "name"
        SRT "*=1"
        WRITE_INT "start"

MATCH   ">*"
        SRT "* *=*1"
        WRITE "fasta_id"

MATCH   "*altitude=*"
        SRT "*altitude\=*] *=*2"
        WRITE "altitude_slv"

MATCH   "*bio-material=*"
        SRT "*bio-material\=*] *=*2"
        WRITE "bio_material"

MATCH   "*clone-lib=*"
        SRT "*clone-lib\=*] *=*2"
        WRITE "clone_lib"

MATCH   "*strain=*"
        SRT "*strain\=*] *=*2"
        WRITE "strain"

MATCH   "*fingerprint_lib=*"
        SRT "*fingerprint_lib\=*] *=*2"
        WRITE "fingerprint_lib"

MATCH   "*chlorophyll=*"
        SRT "*chlorophyll\=*] *=*2"
        WRITE "chlorophyll_slv"

MATCH   "*collected-by=*"
        SRT "*collected-by\=*] *=*2"
        WRITE "collected_by"

MATCH   "*collection-date=*"
        SRT "*collection-date\=*] *=*2"
        WRITE "collection_date"

MATCH   "*collection_time=*"
        SRT "*collection_time\=*] *=*2"
        WRITE "collection_time_slv"

MATCH   "*country=*"
        SRT "*country\=*] *=*2"
        WRITE "country"

MATCH   "*culture-collection=*"
        SRT "*culture-collection\=*] *=*2"
        WRITE "culture_collection"

MATCH   "*depth=*"
        SRT "*depth\=*] *=*2"
        WRITE "depth_slv"

MATCH   "*dissolved_oxygen=*"
        SRT "*dissolved_oxygen\=*] *=*2"
        WRITE "dissolved_oxygen_slv"

MATCH   "*DOC=*"
        SRT "*DOC\=*] *=*2"
        WRITE "DOC_slv"

MATCH   "*environmental-sample=*"
        SRT "*environmental-sample\=*] *=*2"
        WRITE "environmental_sample"

MATCH   "*fwd-pcr-primer-seq=*"
        SRT "*fwd-pcr-primer-seq\=*] *=*2"
        WRITE "fwd_pcr_primer_seq"

MATCH   "*geodetic_datum=*"
        SRT "*geodetic_datum\=*] *=*2"
        WRITE "geodetic_datum_slv"

MATCH   "*habitat=*"
        SRT "*habitat\=*] *=*2"
        WRITE "habitat_slv"

MATCH   "*haplotype=*"
        SRT "*haplotype\=*] *=*2"
        WRITE "haplotype"

MATCH   "*identified-by=*"
        SRT "*identified-by\=*] *=*2"
        WRITE "identified_by"

MATCH   "*isolation-source=*"
        SRT "*isolation-source\=*] *=*2"
        WRITE "isolation_source"

MATCH   "*lab-host=*"
        SRT "*lab-host\=*] *=*2"
        WRITE "lab_host"

MATCH   "*lat_lon_details=*"
        SRT "*lat_lon_details\=*] *=*2"
        WRITE "lat_lon_details_slv"

MATCH   "*lat-lon=*"
        SRT "*lat-lon\=*] *=*2"
        WRITE "lat_lon"

MATCH   "*metagenomic=*"
        SRT "*metagenomic\=*] *=*2"
        WRITE "metagenomic"

MATCH   "*nitrate=*"
        SRT "*nitrate\=*] *=*2"
        WRITE "nitrate_slv"

MATCH   "*pH=*"
        SRT "*pH\=*] *=*2"
        WRITE "pH_slv"

MATCH   "*phosphate=*"
        SRT "*phosphate\=*] *=*2"
        WRITE "phosphate_slv"

MATCH   "*plasmid-name=*"
        SRT "*plasmid-name\=*] *=*2"
        WRITE "plasmid_name"

MATCH   "*project_name=*"
        SRT "*project_name\=*] *=*2"
        WRITE "project_name_slv"

MATCH   "*POC=*"
        SRT "*POC\=*] *=*2"
        WRITE "POC_slv"

MATCH   "*rev-pcr-primer-seq=*"
        SRT "*rev-pcr-primer-seq\=*] *=*2"
        WRITE "rev_pcr_primer_seq"

MATCH   "*salinity=*"
        SRT "*salinity\=*] *=*2"
        WRITE "salinity_slv"

MATCH   "*sample_identifier=*"
        SRT "*sample_identifier\=*] *=*2"
        WRITE "sample_identifier_slv"

MATCH   "*sample_material=*"
        SRT "*sample_material\=*] *=*2"
        WRITE "sample_material_slv"

MATCH   "*sample_volume=*"
        SRT "*sample_volume\=*] *=*2"
        WRITE "sample_volume_slv"

MATCH   "*silicate=*"
        SRT "*silicate\=*] *=*2"
        WRITE "silicate_slv"

MATCH   "*specific-host=*"
        SRT "*specific-host\=*] *=*2"
        WRITE "specific_host"

MATCH   "*specimen-voucher=*"
        SRT "*specimen-voucher\=*] *=*2"
        WRITE "specimen_voucher"

MATCH   "*sub-species=*"
        SRT "*sub-species\=*] *=*2"
        WRITE "sub_species"

MATCH   "*temperature=*"
        SRT "*temperature\=*] *=*2"
        WRITE "temperature_slv"

MATCH   "*organism=*"
        SRT "*organism\=*] *=*2"
        WRITE "full_name"

SEQUENCEAFTER   "*"
SEQUENCESRT     ""
SEQUENCEACI     "remove(".-0123456789 /")"
SEQUENCECOLUMN   0
SEQUENCEEND     ">*"

# DONT_GEN_NAMES
CREATE_ACC_FROM_SEQUENCE

END     "//"