9b6958624673a00fdbe8447b7167e08301fd84bb baertsch Fri May 20 13:31:58 2011 -0700 retro track changes to add ucscRetroOrtho table and hgc, hgTrackUI changes. diff --git src/hg/lib/ucscRetroInfo.sql src/hg/lib/ucscRetroInfo.sql index 1121847..0245596 100644 --- src/hg/lib/ucscRetroInfo.sql +++ src/hg/lib/ucscRetroInfo.sql @@ -1,67 +1,64 @@ -# retroMrnaInfo.sql was originally generated by the autoSql program, which also -# generated retroMrnaInfo.c and retroMrnaInfo.h. This creates the database representation of +# ucscRetroInfo.sql was originally generated by the autoSql program, which also +# generated ucscRetroInfo.c and ucscRetroInfo.h. This creates the database representation of # an object which can be loaded and saved from RAM in a fairly # automatic way. #Retrogenes based on cDNA alignments that are expressed or processed pseudogenes. +drop table ucscRetroInfo; CREATE TABLE ucscRetroInfo ( chrom varchar(255) not null, # Reference sequence chromosome or scaffold col1 chromStart int unsigned not null, # pseudogene alignment start position col2 chromEnd int unsigned not null, # pseudogene alignment end position col3 name varchar(255) not null, # Name of pseudogene col4 score int unsigned not null, # score of pseudogene with gene col5 strand char(2) not null, # + or - thickStart int unsigned not null, # Start of where display should be thick (start codon) thickEnd int unsigned not null, # End of where display should be thick (stop codon) reserved int unsigned not null, # Always zero for now blockCount int not null, # Number of blocks blockSizes longblob not null, # Comma separated list of block sizes chromStarts longblob not null, # Start positions relative to chromStart retroExonCount int not null, # number of exons in retroGene col13 axtScore int not null, # blastz score, parent mrna aligned to pseudogene col14 type varchar(255) not null, # type of evidence col15 gChrom varchar(255) not null, # Chromosome name col16 gStart int not null, # gene alignment start position col17 gEnd int not null, # gene alignment end position col18 gStrand char(2) not null, # strand of gene col19 parentSpliceCount int unsigned not null, # # of splice sites in parent gene col20 geneOverlap int unsigned not null, # bases overlapping col21 polyA int unsigned not null, # count of As in polyA col22 polyAstart int not null, # start of polyA, relative to end of pseudogene col23 exonCover int not null, # number of exons in Gene covered col24 intronCount int unsigned not null, # number of introns in pseudogene col25 bestAliCount int unsigned not null, # number of good mrnas aligning col26 matches int unsigned not null, # matches + repMatches col27 qSize int unsigned not null, # aligning bases in pseudogene col28 qEnd int unsigned not null, # end of cdna alignment col29 tReps int unsigned not null, # repeats in gene col30 - overlapRhesus int not null, # percent of retro that breaks net relative to Rhesus col31 - overlapMouse int not null, # percent of retro that breaks net relative to Mouse col32 - coverage int unsigned not null, # % of bases that align to gene col33 - label int not null, # 1=pseudogene,-1 not pseudogene -2 expressed retroGene col34 - milliBad int unsigned not null, # milliBad score, pseudogene aligned to genome col35 - oldScore int unsigned not null, # another heuristic col36 - oldIntronCount int not null, # old simple intron count col37 - processedIntrons int not null, # count of introns removed via retrotransposition col38 - conservedSpliceSites int not null, # conserved splice site count col39 - maxOverlap int not null, # largest overlap with another mrna col40 - refSeq varchar(255) not null, # Name of closest regSeq to gene col41 - rStart int not null, # refSeq alignment start position col42 - rEnd int not null, # refSeq alignment end position col43 - mgc varchar(255) not null, # Name of closest mgc to gene col44 - mStart int not null, # mgc alignment start position col45 - mEnd int not null, # mgc alignment end position col46 - kgName varchar(255) not null, # Name of closest knownGene to gene col47 - kStart int not null, # kg alignment start position col48 - kEnd int not null, # kg alignment end position col49 - overName varchar(255) not null, # name of overlapping mrna col50 - overStart int not null, # overlapping mrna start position col51 - overExonCover int not null, # count of overlapping mrna exons col52 - overStrand char(2) not null, # strand of overlapping mrna col53 - overlapDog int not null, # percent of retro that breaks net relative to dog col54 - posConf float not null, # pvalue for positive col55 - polyAlen int unsigned not null, # length of polyA col56 - kaku float not null, # ratio of substitutions between coding and utr wrt parent gene + coverage int unsigned not null, # % of bases that align to gene col31 + label int not null, # 1=pseudogene,-1 not pseudogene -2 expressed retroGene col32 + milliBad int unsigned not null, # milliBad score, pseudogene aligned to genome col33 + oldScore int unsigned not null, # another heuristic col34 + oldIntronCount int not null, # old simple intron count col35 + processedIntrons int not null, # count of introns removed via retrotransposition col36 + conservedSpliceSites int not null, # conserved splice site count col37 + maxOverlap int not null, # largest overlap with another mrna col38 + refSeq varchar(255) not null, # Name of closest regSeq to gene col39 + rStart int not null, # refSeq alignment start position col40 + rEnd int not null, # refSeq alignment end position col41 + mgc varchar(255) not null, # Name of closest mgc to gene col42 + mStart int not null, # mgc alignment start position col43 + mEnd int not null, # mgc alignment end position col44 + kgName varchar(255) not null, # Name of closest knownGene to gene col45 + kStart int not null, # kg alignment start position col46 + kEnd int not null, # kg alignment end position col47 + overName varchar(255) not null, # name of overlapping mrna col48 + overStart int not null, # overlapping mrna start position col49 + overExonCover int not null, # count of overlapping mrna exons col50 + overStrand char(2) not null, # strand of overlapping mrna col51 + posConf float not null, # pvalue for positive col52 + polyAlen int unsigned not null, # length of polyA col53 #Indices PRIMARY KEY(name) );