# some simple testing stuff

SET emboss_qadata /homes/pmr/hgmp/test

SET emboss_timetoday "2005-07-15 12:00:00"

#######################################
# Standard test databases
#######################################

# Should be uncommented in the installed copy of emboss.default

##################################################################
# Test Databases
# Used by the qatest.pl script to test an EMBOSS installation.
# Comment them out if you do not want your users to use them.
# Examples in the EMBOSS documentation should all run by using
# TEMBL: in place of EMBL:, TSW: in place of SW:, and so on.
##################################################################


# swissprot (Puffer fish entries)
# =========

DB tsw [ type: P dir: $emboss_tempdata/swiss
   method: emblcd format: swiss release: 36
   fields: "sv des org key"
   comment: "Swissprot native format with EMBL CD-ROM index" ]

# swnew (Puffer fish entries)
# =====

DB tswnew [ type: P dir: $emboss_tempdata/swnew
   method: emblcd format: swiss release: 37 
   fields: "sv des org key"
   comment: "Swissnew as 3 files in native format with EMBL CD-ROM index" ]

# wormpep (cosmid ZK637)
# =======

DB twp [ type: P dir: $emboss_tempdata/wormpep
   method: emblcd format: fasta release: 16 
   fields: "des"
   comment: "EMBL new in native format with EMBL CD-ROM index" ]

# embl (worm cosmid ZK637 and a few other entries)
# ====

DB tembl [ type: N dir: $emboss_tempdata/embl
   method: emblcd format: embl release: 57 
   fields: "sv des org key"
   comment: "EMBL in native format with EMBL CD-ROM index" ]

# pir (cytochrome C plus first entries in other divisions)
# ===

DB tpir [ type: P dir: $emboss_tempdata/pir
   method: gcg
   file: pir*.seq
   format: nbrf
   fields: "des org key"
   comment: "PIR using NBRF access for 4 files" ]

# Genbank (Canadian EMBnet node - so long as they are running SRS version 6)
# =======

DB tgb [ type: N method: srswww format: genbank
   url: "http://www.cbr.nrc.ca/srs6bin/cgi-bin/wgetz"
   dbalias: genbank
   fields: "sv des org key"
   comment: "Genbank IDs" ]

# Genbank (local copy of the TEMBL entries from Genbank)
# =======

DB tgenbank [ type: N dir: $emboss_tempdata/genbank
   method: emblcd format: genbank release: 01 
   fields: "sv des org key"
   comment: "GenBank in native format with EMBL CD-ROM index" ]

#######################################
### 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"
]

DB qanxflat  [ type: N format: embl method: emboss
  dir: $emboss_qadata/embl
  indexdir: $emboss_qadata/qa/dbxflat-ex-keep
  dbalias: embl
  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"
]

DB qapxflat  [ type: P format: swiss method: emboss
  dir: $emboss_qadata/swnew
  indexdir: $emboss_qadata/qa/dbxflat-swiss-keep
  dbalias: swnew
  comment: "Swissnew flatfiles"
]

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

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

DB qanxflatall  [ type: N format: embl method: emboss
  dir: $emboss_qadata/embl
  indexdir: $emboss_qadata/qa/dbxflat-all-keep
  fields: "des org key"
  dbalias: embl
  comment: "EMBL flatfiles, all fields indexed"
]

###########################################
### 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 EMBOSS, FASTA format data
###########################################

DB qanxfasta  [ type: N format: fasta method: emboss
  dir: $emboss_qadata/data
  indexdir: $emboss_qadata/qa/dbxfasta-ex-keep
  dbalias: emrod
  comment: "FASTA file EMBL rodents"
]

DB qapxfasta  [ type: P format: fasta method: emboss
  dir: $emboss_qadata/data
  indexdir: $emboss_qadata/qa/dbxfasta-swiss-keep
  dbalias: swnew
  comment: "FASTA file swissnew entries"
]

DB qawxfasta  [ type: N format: fasta method: emboss
  dir: $emboss_qadata/data
  indexdir: $emboss_qadata/qa/dbxfasta-worm-keep
  dbalias: worm
  comment: "FASTA file wormpep entries"
]

DB qanxfastaall  [ type: N format: fasta method: emboss
  dir: $emboss_qadata/data
  indexdir: $emboss_qadata/qa/dbxfasta-allsys-keep
  fields: "sv des"
  comment: "FASTA file EMBL rodents, all fields indexed"
  dbalias: emrod
]

#######################
### 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"
]

DB qapir  [ type: P format: nbrf method: gcg
  dir: $emboss_qadata/pir
  indexdir: $emboss_qadata/qa/dbigcg-pir-keep
  comment: "PIR"
]

DB qapirexc  [ type: N format: nbrf method: gcg
  dir: $emboss_qadata/pir
  exclude: pir1.*
  indexdir: $emboss_qadata/qa/dbigcg-pir-keep
  comment: "PIR"
]

DB qapirinc  [ type: P format: nbrf method: gcg
  dir: $emboss_qadata/pir
  file: pir1.*
  exclude: *
  indexdir: $emboss_qadata/qa/dbigcg-pir-keep
  comment: "PIR"
]

DB qapirall  [ type: P format: nbrf method: gcg
  dir: $emboss_qadata/pir
  indexdir: $emboss_qadata/qa/dbigcg-pirall-keep
  comment: "PIR"
  fields: "des org key"
]

###########################
### access method EMBOSSGCG
###########################

DB qanxgcg  [ type: N format: embl method: embossgcg
  dir: $emboss_qadata/embl
  indexdir: $emboss_qadata/qa/dbxgcg-ex-keep
  dbalias: embl
  comment: "GCG format EMBL"
]

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

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

DB qanxgcgall  [ type: N format: embl method: embossgcg
  dir: $emboss_qadata/embl
  indexdir: $emboss_qadata/qa/dbxgcg-allsys-keep
  fields: "sv des org key"
  dbalias: embl
  comment: "GCG format EMBL"
]

DB qaxpir  [ type: P format: nbrf method: embossgcg
  dir: $emboss_qadata/pir
  indexdir: $emboss_qadata/qa/dbxgcg-pir-keep
  dbalias: pir
  comment: "PIR"
]

DB qaxpirexc  [ type: N format: nbrf method: embossgcg
  dir: $emboss_qadata/pir
  exclude: pir1.*
  indexdir: $emboss_qadata/qa/dbxgcg-pir-keep
  dbalias: pir
  comment: "PIR"
]

DB qaxpirinc  [ type: P format: nbrf method: embossgcg
  dir: $emboss_qadata/pir
  file: pir1.*
  exclude: *
  indexdir: $emboss_qadata/qa/dbxgcg-pir-keep
  dbalias: pir
  comment: "PIR"
]

DB qaxpirall  [ type: P format: nbrf method: embossgcg
  dir: $emboss_qadata/pir
  indexdir: $emboss_qadata/qa/dbxgcg-pirall-keep
  fields: "des org key"
  dbalias: pir
  comment: "PIR"
]

#####################
### 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"
]

############################
### access method direct ###
############################

# embl (worm cosmid ZK637 and a few other entries)
# ====

DB temblall [ type: N dir: "$emboss_tempdata/embl"
   method: direct format: embl release: 57 
   fields: "sv des org key"
   comment: "EMBL in native format with EMBL CD-ROM index"
  filename: "*.dat"
]

# embl (worm cosmid ZK637 and a few other entries)
# ====

DB temblvrt [ type: N dir: "$emboss_tempdata/embl"
   method: direct format: embl release: 57 
   fields: "sv des org key"
   comment: "EMBL in native format with EMBL CD-ROM index"
  filename: "hum*.dat rod*.dat vrt*.dat"
]

# embl (worm cosmid ZK637 and a few other entries)
# ====

DB temblrest [ type: N dir: "$emboss_tempdata/embl"
   method: direct format: embl release: 57 
   fields: "sv des org key"
   comment: "EMBL in native format with EMBL CD-ROM index"
   filename: "*.dat"
   exclude: "hum*.dat rod*.dat vrt*.dat"
]

RES embl [ type: "Index" ]
RES swnew [ type: "Index" ]
RES pir [ type: "Index" ]
