#!/bin/sh
# 2 other
# 112 vertebrate_other
# 132 vertebrate_mammalian
# 170 plant
# 183 protozoa
# 275 invertebrate
# 474 archaea
# 941 fungi
# 32804 bacteria
export inside="/hive/data/inside/ncbi/genomes/genbank"
export topDir="/hive/data/inside/ncbi/genomes/genbank/hubs"
export dirLimit=1000
for groupName in bacteria
do
cd "${topDir}"
partsIndex="${topDir}/${groupName}/bacteria.ncbi.html"
rm -f "${partsIndex}"
printf "%s\n" \
'
Bacterial assembly hubs
Bacterial assembly hub
bacterial genome assembly hubs
Each link is a set of about 1,000 genomes in an assembly hub
' > "${partsIndex}"
rm -fr "/dev/shm/${groupName}"
mkdir -p "/dev/shm/${groupName}"
tf="/dev/shm/${groupName}/src.${groupName}.$$"
grep "/${groupName}/" ../checksOK.list | sort -f > ${tf}
split -l $dirLimit -d ${tf} "/dev/shm/${groupName}/${groupName}."
for F in /dev/shm/${groupName}/${groupName}.*
do
firstSpecies=`head -1 ${F} | tail -1 | sed -e "s#./${groupName}/##; s#/latest_assembly_versions/# #; s#/.*##;"`
lastSpecies=`tail -1 ${F} | sed -e "s#./${groupName}/##; s#/latest_assembly_versions/# #; s#/.*##;"`
N=`basename ${F} | sed -e "s/${groupName}.//;"`
wrkDir="${topDir}/${groupName}/${N}"
mkdir -p ${wrkDir}
printf "- %s to %s
\n" "$N" "${groupName}" "${N}" "$firstSpecies" "$lastSpecies" >> "${partsIndex}"
printf "%s\n" "$N" 1>&2
rm -f ${wrkDir}/groups.txt
ln -s ../../groups.txt ${wrkDir}/groups.txt
# XXX restore this when new order.tab files are needed
# XXX if [ 0 -eq 1 ]; then
cat ${F} | sed -e 's#^./##;' | \
while read F
do
dirName=`dirname ${F}`
srcDir="${inside}/${dirName}"
B=`basename ${F} | sed -e 's/.checkAgpStatusOK.txt//;'`
nameDefs="${srcDir}/${B}.names.tab"
trackDb="${srcDir}/${B}.trackDb.ncbi.txt"
chromSizes="${srcDir}/${B}.ncbi.chrom.sizes"
if [ -s "${trackDb}" ]; then
orgName=`grep -v "^#" "${nameDefs}" | cut -f2`
sciName=`grep -v "^#" "${nameDefs}" | cut -f5`
asmDate=`grep -v "^#" "${nameDefs}" | cut -f9`
asmName=`grep -v "^#" "${nameDefs}" | cut -f4`
# fields 1 2 3 day month year
printf "%s" "${asmDate}" | tr '[ ]' '[\t]'
# fields 4 5 6 7
printf "\t%s" "${orgName}" "${sciName}" "${asmName}" "${F}"
printf "\n"
grep -v "^#" "${srcDir}/${B}.build.stats.txt" >> ${wrkDir}/${groupName}.${N}.total.stats.txt
fi
done > ${wrkDir}/${groupName}.${N}.order.tab
# processing one set list into order.tab
directoryCount=`cat "${F}" | wc -l`
totalContigs=`cut -f1 ${wrkDir}/${groupName}.${N}.total.stats.txt | ave stdin | grep -w total | awk '{print $NF}' | sed -e 's/.000000//'`
totalSize=`cut -f2 ${wrkDir}/${groupName}.${N}.total.stats.txt | ave stdin | grep -w total | awk '{print $NF}' | sed -e 's/.000000//'`
orgCount=`cut -f4 ${wrkDir}/${groupName}.${N}.order.tab | sort -u | wc -l`
asmCount=`cut -f6 ${wrkDir}/${groupName}.${N}.order.tab | sort -u | wc -l`
orgAsmCount=`cut -f4,6 ${wrkDir}/${groupName}.${N}.order.tab | sort -u | wc -l`
duplicates=`echo "${directoryCount}" "${asmCount}" | awk '{printf "%d", $1-$2}'`
printf "%s: assemblies: %s, genomes: %s, duplicates: %s\n" \
"$groupName.${N}" "$asmCount" "$orgCount" "$duplicates" 1>&2
rm -f "${wrkDir}/hub.ncbi.txt"
printf "hub %s\n" "${groupName}.${N}" > "${wrkDir}/hub.ncbi.txt"
printf "shortLabel Genbank '%s'\n" "${groupName}.${N}" >> "${wrkDir}/hub.ncbi.txt"
printf "longLabel Synthetic genomes from Genbank, category '%s'\n" "${groupName}.${N}" >> "${wrkDir}/hub.ncbi.txt"
printf "genomesFile genomes.ncbi.txt\n" >> "${wrkDir}/hub.ncbi.txt"
printf "email genome-www@soe.ucsc.edu\n" >> "${wrkDir}/hub.ncbi.txt"
printf "descriptionUrl %s.html\n" "${groupName}.${N}" >> "${wrkDir}/hub.ncbi.txt"
rm -f "${wrkDir}/genomes.ncbi.txt"
sort -t' ' -k6,6 -u ${wrkDir}/${groupName}.${N}.order.tab \
| sort -t' ' -k4,4f -k3,3nr -k2,2Mr -k1,1nr | cut -f7 | while read F
do
dirName=`dirname ${F}`
srcDir="${inside}/${dirName}"
B=`basename ${F} | sed -e 's/.checkAgpStatusOK.txt//;'`
nameDefs="${srcDir}/${B}.names.tab"
trackDb="${srcDir}/${B}.trackDb.ncbi.txt"
chromSizes="${srcDir}/${B}.ncbi.chrom.sizes"
if [ -d "${srcDir}" -a -s "${trackDb}" -a -s "${chromSizes}" -a -s "${nameDefs}" ]; then
defaultChr=`head -1 "${chromSizes}" | cut -f1`
chrName=`head -1 "${chromSizes}" | cut -f1`
chrSize=`head -1 "${chromSizes}" | cut -f2`
halfWidth=`echo $chrSize | awk '{oneTenth=$1/10; if (oneTenth > 1000000) { print "1000000"; } else {printf "%d", oneTenth;}}'`
defaultPos=`echo $chrName $chrSize $halfWidth | awk '{printf "%s:%d-%d", $1, ($2/2 - $3), ($2/2 + $3)}'`
orgName=`grep -v "^#" "${nameDefs}" | cut -f2`
sciName=`grep -v "^#" "${nameDefs}" | cut -f5`
asmDate=`grep -v "^#" "${nameDefs}" | cut -f9`
asmName=`grep -v "^#" "${nameDefs}" | cut -f4`
printf "\ngenome %s\n" "$B" >> "${wrkDir}/genomes.ncbi.txt"
printf "description %s/%s\n" "${asmDate}" "${asmName}" >> "${wrkDir}/genomes.ncbi.txt"
printf "trackDb %s/%s.trackDb.ncbi.txt\n" "$B" "${B}" >> "${wrkDir}/genomes.ncbi.txt"
printf "groups groups.txt\n" >> "${wrkDir}/genomes.ncbi.txt"
printf "twoBitPath %s/%s.ncbi.2bit\n" "${B}" "${B}" >> "${wrkDir}/genomes.ncbi.txt"
printf "organism %s\n" "${orgName}" >> "${wrkDir}/genomes.ncbi.txt"
printf "scientificName %s\n" "${sciName}" >> "${wrkDir}/genomes.ncbi.txt"
printf "defaultPos %s\n" "${defaultPos}" >> "${wrkDir}/genomes.ncbi.txt"
printf "htmlPath %s/%s.description.html\n" "${B}" "${B}" >> "${wrkDir}/genomes.ncbi.txt"
rm -f "${wrkDir}/${B}"
ln -s "${srcDir}" "${wrkDir}/${B}"
printf "%s\n" "${B}" 1>&2
# ./hubHtml.pl "${srcDir}/${B}" >> "${groupName}/${groupName}.html"
fi
done # processing one order.tab into a genomes.ncbi.txt file
# XXX fi # temporarily off
done # processing one set list
printf "%s\n" '
' >>"${partsIndex}"
done # processing: for groupName in bacteria
exit $?
# ./bacteria/Pasteurella_multocida/latest_assembly_versions/GCA_000219315.2_ASM21931v2/GCA_000219315.2_ASM21931v2.checkAgpStatusOK.txt