# some simple testing stuff

SET emboss_qadata /srsuser/rice/hgmp/emboss/test

#######################################
### Access method EMBLCD, flatfile data
#######################################

# Nucleotide data (1 file)
# ===============

DB qanflat  [ type: N format: embl method: emblcd
  dir: $emboss_qadata/embl
  indexdir: $emboss_qadata/qa/dbiflat-ex-keep
  comment: "EMBL flatfiles"
]

# Protein data (3 files)
# ============

DB qapflat  [ type: P format: swiss method: emblcd
  dir: $emboss_qadata/swnew
  indexdir: $emboss_qadata/qa/dbiflat-swiss-keep
  comment: "Swissnew flatfiles"
]

DB qapflatexc  [ type: P format: swiss method: emblcd
  dir: $emboss_qadata/swnew
  exclude: upd_seq.dat
  indexdir: $emboss_qadata/qa/dbiflat-swiss-keep
  comment: "Swissnew flatfiles, no updated sequence file"
]

DB qapflatinc  [ type: P format: swiss method: emblcd
  dir: $emboss_qadata/swnew
  file: upd_seq.dat
  exclude: *.dat
  indexdir: $emboss_qadata/qa/dbiflat-swiss-keep
  comment: "Swissnew flatfiles, only updated sequence file"
]

DB qapflatall  [ type: P format: swiss method: emblcd
  dir: $emboss_qadata/swnew
  indexdir: $emboss_qadata/qa/dbiflat-swiss-allsys-keep
  comment: "Swissnew flatfiles, all fields indexed"
  fields: "sv des org key"
]

###########################################
### Access method EMBLCD, FASTA format data
###########################################

DB qanfasta  [ type: N format: fasta method: emblcd
  dir: $emboss_qadata/data
  indexdir: $emboss_qadata/qa/dbifasta-ex-keep
  comment: "FASTA file EMBL rodents"
]

DB qapfasta  [ type: P format: fasta method: emblcd
  dir: $emboss_qadata/data
  indexdir: $emboss_qadata/qa/dbifasta-swiss-keep
  comment: "FASTA file swissnew entries"
]

DB qawfasta  [ type: N format: fasta method: emblcd
  dir: $emboss_qadata/data
  indexdir: $emboss_qadata/qa/dbifasta-worm-keep
  comment: "FASTA file wormpep entries"
]

DB qanfastaall  [ type: N format: fasta method: emblcd
  dir: $emboss_qadata/data
  indexdir: $emboss_qadata/qa/dbifasta-allsys-keep
  comment: "FASTA file EMBL rodents, all fields indexed"
  fields: "sv des"
]

#######################
### Access method BLAST
#######################

DB qapblast  [ type: P format: ncbi method: blast
  dir: $emboss_qadata/data
  indexdir: $emboss_qadata/qa/dbiblast-ex-keep
  comment: "BLAST swissnew"
]

DB qapblastsplit  [ type: P format: ncbi method: blast
  dir: $emboss_qadata/data
  indexdir: $emboss_qadata/qa/dbiblast-split-keep
  comment: "BLAST swissnew split in 5 files"
]

DB qapblastsplitexc  [ type: P format: ncbi method: blast
  dir: $emboss_qadata/data
  exclude: swsplit.02.*
  indexdir: $emboss_qadata/qa/dbiblast-split-keep
  comment: "BLAST swissnew split in 5 files, not file 02"
]

DB qapblastsplitinc  [ type: P format: ncbi method: blast
  dir: $emboss_qadata/data
  file: swsplit.02.*
  exclude: *
  indexdir: $emboss_qadata/qa/dbiblast-split-keep
  comment: "BLAST swissnew split in 5 files, only file 02"
]

DB qapblastall  [ type: P format: ncbi method: blast
  dir: $emboss_qadata/data
  indexdir: $emboss_qadata/qa/dbiblast-allsys-keep
  comment: "BLAST swissnew, all fields indexed"
  fields: "sv des"
]

#####################
### access method GCG
#####################

DB qangcg  [ type: N format: embl method: gcg
  dir: $emboss_qadata/embl
  indexdir: $emboss_qadata/qa/dbigcg-ex-keep
  comment: "GCG format EMBL"
]

DB qangcgexc  [ type: N format: embl method: gcg
  dir: $emboss_qadata/embl
  exclude: eem_ba1.*
  indexdir: $emboss_qadata/qa/dbigcg-ex-keep
  comment: "GCG format EMBL without prokaryotes"
]

DB qangcginc  [ type: N format: embl method: gcg
  dir: $emboss_qadata/embl
  file: eem_ba1.*
  exclude: *
  indexdir: $emboss_qadata/qa/dbigcg-ex-keep
  comment: "GCG format EMBL only prokaryotes"
]

DB qangcgall  [ type: N format: embl method: gcg
  dir: $emboss_qadata/embl
  indexdir: $emboss_qadata/qa/dbigcg-allsys-keep
  comment: "GCG format EMBL"
  fields: "sv des org key"
]

#####################
### access method SRS
#####################

DB qasrs [ type: N format: embl method: srs
  dbalias: embl
  fields: "sv des org"     # key omitted to test error messages
  comment: "EMBL in local srs installation"
]

##########################
### access method SRSFASTA
##########################

DB qasrsfasta [ type: N format: fasta method: srsfasta
  dbalias: embl
  fields: "sv des org key"
  comment: "EMBL in local srs installation, fasta format"
]

########################
### access method SRSWWW
########################

DB qasrswww [ type: N format: embl method: srswww
  dbalias: embl
  fields: "sv des org key"
  url: http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz
  comment: "Remote SRS web server"
]
