src/utils/qa/chain2.csh 1.12
1.12 2009/07/09 21:18:18 kuhn
dropped exit command that was in there for debugging
Index: src/utils/qa/chain2.csh
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/chain2.csh,v
retrieving revision 1.11
retrieving revision 1.12
diff -b -B -U 1000000 -r1.11 -r1.12
--- src/utils/qa/chain2.csh 9 Jul 2009 21:17:28 -0000 1.11
+++ src/utils/qa/chain2.csh 9 Jul 2009 21:18:18 -0000 1.12
@@ -1,204 +1,202 @@
#!/bin/tcsh
source `which qaConfig.csh`
###############################################
#
# 03-28-04 & 10-26-2005
# Checks chain tracks.
# Written by Bob Kuhn - augmented by Ann Zweig.
# Runs slow processes (quick processes are in chain.csh).
#
###############################################
onintr cleanup
set db=""
set split=""
set trackname=""
if ( $#argv != 2 ) then
# no command line args
echo
echo " runs test suite on chain track (on both regular and Link tables)"
echo " expects trackname in chrN_chainOrg format."
echo " though it now works for chainOrg format assemblies"
echo " this can take a long time."
echo
echo " usage: database trackname"
echo " e.g. chain2.csh mm7 chrN_chainXenTro1 > & mm7.chain2.xenTro1 &"
echo " or chain2.csh anoCar1 chainXenTro1 > & anoCar1.chain.xenTro1 &"
echo
exit
else
set db=$argv[1]
set trackname=$argv[2]
endif
set track=`echo $trackname | sed -e "s/chrN_//"`
set Org=`echo $track | sed -e "s/chain//"`
set split=`getSplit.csh $db chain$Org hgwdev`
echo "using database $db "
echo "trackname: $trackname"
echo "track: $track"
echo "Org: $Org"
# -------------------------------------------------
# get chroms from chromInfo:
getChromlist.csh $db > $db.chromlist$$
if ( $split != "unsplit" ) then
cat $db.chromlist$$
endif
# ------------------------------------------------
# featureBits
echo "*~*~*~*~*~*~*~*~*~*~*~*~*~*"
echo "run featureBits"
echo
runBits.csh $db $track
# -------------------------------------------------
# check sort
# note: chain*Link tables do not need to be sorted if they have an index
echo
echo "*~*~*~*~*~*~*~*~*~*~*~*~*~*"
echo "check sort:"
positionalTblCheck -verbose=0 $db chain$Org
if ( ! $status ) then
echo "sort is ok"
endif
echo
-exit
-
# -------------------------------------------------
# check ends for off-end coords:
# slow:
echo
echo "*~*~*~*~*~*~*~*~*~*~*~*~*~*"
echo "looking for annotations off the end of the chrom"
rm -f $db.$track.offEnd
if ( $split == "unsplit" ) then
checkOffend.csh $db $trackname
else
foreach chrom (`cat $db.chromlist$$`)
# echo " chrom: $chrom"
# echo " chrom_track: ${chrom}_$track"
hgsql -N -e "SELECT chromInfo.chrom, chromInfo.size, \
chromInfo.size - MAX(${chrom}_$track.tEnd) \
FROM chromInfo, ${chrom}_$track \
WHERE chromInfo.chrom = ${chrom}_$track.tName \
GROUP BY chromInfo.chrom" $db >> $db.$track.offEnd
end
echo "rows from $db that are off the end of the chrom:"
awk '{if($3<0) {print $3} }' $db.$track.offEnd
echo "expect blank here - if not, check the file $db.$track.offEnd"
endif
# -------------------------------------------------
# check to see if coords in other assembly are off the end.
set otherDb=`echo $Org | perl -wpe '$_ = lcfirst($_)'`
hgsql -N -e "SELECT size, chrom FROM chromInfo" $otherDb | sort -nr > $otherDb.size
if ( $split == "unsplit" ) then
echo "check to see if qSize matches coords in other assembly."
hgsql -N -e "SELECT DISTINCT qSize, qName FROM chain$Org \
GROUP by qSize" $db | sort -nr > $db.query.size
commTrio.csh $db.query.size $otherDb.size
echo "expect zero for $db.query.size"
else
# not really needed and too complicated here.
# the chances of this being broken are very small
# foreach chrom (`cat $db.chromlist$$`)
# hgsql -N -e "SELECT DISTINCT qSize, qName FROM ${chrom}_chain$Org \
# GROUP by qSize" $db | sort -nr > ${chrom}.query.size
# commTrio.csh ${chrom}.query.size $otherDb.size
# end
endif
# -------------------------------------------------
# for unsplit: checking that all chroms are used
if ( $split == "unsplit" ) then
echo
echo "*~*~*~*~*~*~*~*~*~*~*~*~*~*"
echo
echo "checking that all chroms (scaffolds) have chains in chain table"
hgsql -N -e "SELECT DISTINCT(tName) FROM $track" $db | sort > $db.$track.chroms
commTrio.csh $db.chromlist$$ $db.$track.chroms
if ( `wc -l $db.chromlist$$.Only | awk '{print $1}'` > 0 ) then
# some chroms have not chains. display links.
# get multiz info for link
set multiz=`hgsql -N -e "SHOW TABLES LIKE 'multiz%'" $db | head -1`
echo "these have no chains:"
if ( $multiz != "" ) then
set multiz="&${multiz}=pack"
endif
foreach seq ( `head -3 $db.chromlist$$.Only` )
echo "http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=$db&position=$seq&chain$Org=pack$multiz"
end
echo "get some DNA from these and see how it blats on $otherDb"
else
echo "all chroms have chains"
endif
endif
# -------------------------------------------------
# Link table: make list of uniq chainIds.
# check if they all exist as chainOrg.id
# dropped this. duplicates joinerCheck
echo
echo "*~*~*~*~*~*~*~*~*~*~*~*~*~*"
echo "running joinerCheck"
joinerCheck -database=$db -keys ~/kent/src/hg/makeDb/schema/all.joiner -identifier=chain${Org}Id
# -------------------------------------------------
# check $trackname for tStart < tEnd
echo
echo "*~*~*~*~*~*~*~*~*~*~*~*~*~*"
echo "check $trackname for tStart < tEnd"
echo "if there is no output here, then it passes."
if ( $split == "unsplit" ) then
set var3=`hgsql -N -e "SELECT COUNT(*) FROM ${track} \
WHERE tStart >= tEnd" $db`
if ($var3 != 0) then
echo "${track} has $var3 records with tStart >= tEnd"
endif
else
foreach chrom (`cat $db.chromlist$$`)
set var3=`hgsql -N -e "SELECT COUNT(*) FROM ${chrom}_${track} \
WHERE tStart >= tEnd" $db`
if ($var3 != 0) then
echo "${chrom}_${track} has $var3 records with tStart >= tEnd"
endif
end
endif
# -------------------------------------------------
# check qStrand values in $track:
# dropped this section. done in chain.csh
# -------------------------------------------------
echo
echo "the end."
cleanup:
rm -f $db.chromlist$$