# UCSCtrackCompare: trackConfiguration file
# author mieg@ncbi.nlm.nih.gov
# 2006_02_15

# This file defines the tracks to be compared
# in the format expected by the program UCSCtrackCompare

# lines beginning with a # and empty lines are ignored

#########################################
# Reference track
# the word REF followed by the symbol of one of the tracks
# this track is then used as the reference track in the
# detailled comparisons exported by  UCSCtrackCompare

REF Gencode

# the reference Must be defined as one of the tracks further down

#########################################
# All tracks
# the program expects 3 columns separated by any number of spaces
# Track name  (p[rotected with "" if it contains a space or another weird character
# 1 or 0 : meaning that the stop codon is/is not included in the CDS coordinates
#          this is a hack because EGASP apparently requested to exclude it but 
#          was not very clear. On the other hand all the public track include it
# File name, absolute file name or relative to the active directory

# An explicit zero : 0 as the first word of the line
# will stop the parsing
# this is the simplest way to work on a singletrack

# This is used for multiple comparison, i just have 'cat' several
# gff files one after the other to create the kingkong giant file
#     kingkong == exhon-hunter + sgp2 + genemark + genzilla 

# "King-Kong"         1  DATA_egasp/kingkong

Gencode               1  DATA_egasp/encodeGencodeGeneKnownOrPutativeOct05
AceView               0  DATA_egasp/encodeEgaspFullAceview

"UP Dogfish"          0  DATA_egasp/encodeEgaspFullDogfish
Ensembl               1  DATA_egasp/encodeEgaspFullEnsembl
Exogean               0  DATA_egasp/encodeEgaspFullExogean

"UP ExonHunter"       1  DATA_egasp/encodeEgaspFullExonhunter
Fgenesh               0  DATA_egasp/encodeEgaspFullFgenesh

"UP GeneID"           1  DATA_egasp/encodeEgaspFullGeneId
"UP GeneMark"         1  DATA_egasp/encodeEgaspFullGenemark 
"UP Jigsaw"           0  DATA_egasp/encodeEgaspFullJigsaw

Pairagon              0  DATA_egasp/encodeEgaspFullPairagonAny

"UP SGP2"             1  DATA_egasp/encodeEgaspFullSgp2
"P Twinscan"          1  DATA_egasp/encodeEgaspFullTwinscan

"UP Augustus"         0  DATA_egasp/encodeEgaspPartAugustusAny

"UP GeneZilla"        0  DATA_egasp/encodeEgaspPartGenezilla
"UP Saga"             0  DATA_egasp/encodeEgaspPartSaga

# PUBLIC

"*KnownGene"          1  DATA_public/knownGene
"*P CCDS"             1  DATA_public/ccdsGene
"*RefSeq"             1  DATA_public/refGene

"*MGC"                1  DATA_public/mgcGenes
"*Ensembl"            1  DATA_public/ensGene
"*AceView"            1  DATA_public/acembly
"*ECgene"             0  DATA_public/ECgene

"*U NscanEst"         1  DATA_public/nscanEstGene
"*UP GenScan"         1  DATA_public/genscan
"*ExonWalk"           1  DATA_public/exonWalk

# drop the remaining redondant  files

0

PairagonMrna          1  DATA_egasp/encodeEgaspFullPairagonMrna
PairagonNovel         1  DATA_egasp/encodeEgaspFullPairagonNovel

"UP AugustusAbinitio" 1  DATA_egasp/encodeEgaspPartAugustusAbinitio
"UP Augustus" ,       1  DATA_egasp/encodeEgaspPartAugustusAny
"UP AugustusDual"     1  DATA_egasp/encodeEgaspPartAugustusDual

"*U NscanEst"         1  DATA_public/nscanEstGene
"*UP SGP"             1  DATA_public/sgpGene

AceCons               1  DATA_egasp/encodeEgaspPartAceCons
AceOther              1  DATA_egasp/encodeEgaspPartAceOther
Spida                 1  DATA_egasp/encodeEgaspFullSpida
vegaGenePublic        1  DATA_public/vegaGene
exoniphyPublic        1  DATA_public/exoniphy

# End of this file
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