Converts DAVID functional annotations to html

david2html

# Converts a tab-separated file containing
# DAVID's functional annotation results to
# Markdown format
# It reports: KEGG and GO terms along with
# the gene symbol and name

FILE=
cut -f 1,2,5,6,7,9 $FILE | awk '
BEGIN{OFS=FS="\t"}NR>1{
print "#"$1
print "##Gene name\n"$2
print "\n"
print "###Biological process"
print "\n"
gsub(/,[ ]{0,1}GO:/, ";GO:", $3);
gsub(/,$/, ";", $3);
for(i=1; i<split($3,a,";");i++){
        print "* "a[i]
}
print "\n"
print "\n"
print "###Cellular component"
print "\n"
gsub(/,[ ]{0,1}GO:/, ";GO:", $4);
gsub(/,$/, ";", $4);
for(i=1; i<split($4,a,";");i++){
        print "* "a[i]
}

print "\n"
print "\n"
print "###Molecular Function"
print "\n"
gsub(/,[ ]{0,1}GO:/, ";GO:", $5);
gsub(/,$/, ";", $5);
for(i=1; i<split($5,a,";");i++){
        print "* "a[i]
}

print "\n"
print "\n"
print "###KEGG pathway"
print "\n"
for(i=1; i<split($6,a,",");i++){
        print "* "a[i]
}

print "\n* * *\n"
}' > ${FILE}.md
pandoc ${FILE}.md -o ${FILE}.html