#!/bin/bash
# the set -x will echo all commands as they execute, for debuggin
# set -x
function tableHeader() {
printf "| Taxon ID |
date | common
name | scientific
name |
biosample | contig
count | genome
size |
N50 size | GC percent |
unknown bases
count/percent |
gene count
bases
percent |
accession | assembly
name | assembly
type |
assembly
level | submitter |
|---|
\n"
}
cd /hive/data/inside/ncbi/genomes/refseq/hubs
declare -A pageTitles
pageTitles=( ["plant"]="Plant assembly hub" \
["fungi"]="Fungi assembly hub" \
["other"]="Other/Synthetic genomic assembly hub" \
["archaea"]="Archaea assembly hub" \
["protozoa"]="Protozoa assembly hub" \
["vertebrate_mammalian"]="Vertebrate Mammalian assembly hub" \
["vertebrate_other"]="non-Mammalian other Vertebrate assembly hub" \
["invertebrate"]="Invertebrates assembly hub" )
export inside="/hive/data/inside/ncbi/genomes/refseq"
# archaea
# fungi
# invertebrate
# plant
# protozoa
# vertebrate_mammalian
# vertebrate_other
# for groupName in archaea fungi invertebrate other plant protozoa vertebrate_mammalian vertebrate_other
# for groupName in archaea fungi invertebrate plant protozoa vertebrate_mammalian vertebrate_other
for groupName in plant protozoa invertebrate vertebrate_other vertebrate_mammalian fungi archaea
do
hubLink="refseq/${groupName}"
pageTitle="${pageTitles["$groupName"]}"
htmlFile="${groupName}/${groupName}.ncbi.html"
rm -f "${htmlFile}"
printf "
%s
%s
\n" "${pageTitle}" "${pageTitle}" > "${htmlFile}"
orgCount=`cut -f4 ${groupName}.order.tab | sort -u | wc -l`
asmCount=`cut -f6 ${groupName}.order.tab | sort -u | wc -l`
totalContigs=`cut -f1 ${groupName}/${groupName}.total.stats.txt | ave stdin | grep -w total | awk '{print $NF}' | sed -e 's/.000000//'`
totalSize=`cut -f2 ${groupName}/${groupName}.total.stats.txt | ave stdin | grep -w total | awk '{print $NF}' | sed -e 's/.000000//'`
printf "\n" >> "${htmlFile}"
tableHeader >> "${htmlFile}"
# every number of lines, print the table header row
export headerFrequency=15
export lineCount=0
export lastHeader=0
sort -t' ' -k6,6 -u ${groupName}.order.tab \
|sort -t' ' -k4,4f -k3,3nr -k2,2Mr -k1,1nr | cut -f7 | sed -e '/^$/d;' \
| while read F
do
dirName=`dirname ${F}`
srcDir="${inside}/${dirName}"
B=`basename ${F} | sed -e 's/.checkAgpStatusOK.txt//;'`
./hubHtml.pl "${hubLink}" "${srcDir}/${B}" >> "${htmlFile}"
printf "%s %s %s %s\n" ${groupName} ${hubLink} ${B} ${srcDir}/${B} 1>&2
lineCount=$(( lineCount+=1 ))
lastHeader=$(( lastHeader+=1 ))
if [ 0 -eq $(( $lineCount % $headerFrequency )) ]; then
tableHeader >> "${htmlFile}"
lastHeader=0
fi
done
if [ $lastHeader -gt 10 ]; then
tableHeader >> "${htmlFile}"
fi
LC_NUMERIC=en_US /usr/bin/printf \
"| total species: %'d |
total assemblies: %'d |
total contigs: %'d |
total nucleotides: %'d |
|---|
\n" $orgCount $asmCount $totalContigs $totalSize \
>> "${htmlFile}"
chmod +x "${htmlFile}"
done