This contains stuff to analyse the UCSC gene set, but
not to build it.  It's mostly stuff hopefully for the paper.

Here's some of what is done

set gd = /cluster/data/hg18/bed/ucsc.10
set wd = ~/kent/src/hg/txPaper

# Make up PFAM info
cut -f 5 $gd/canonical.tab > $gd/canonical.lst
txPaperPfam $gd/ucscGenes.info $gd/ucscPfam.tab $gd/canonical.lst $wd/tables/pfam

# Make up SCOP info
mkdir $wd/tables/scop
awk '{printf("%s\t%s\t%s\t%s\t%s\n", $1, $3, $4, $2, $5);}' $gd/knownToSuper.tab >$wd/tables/scop/ucscScop.tab
txPaperScop $gd/ucscGenes.info $wd/tables/scop/ucscScop.tab $gd/scopDesc.tab $gd/canonical.lst $wd/tables/scop
