I am converting data from LycoCyc 3.3 into a BridgeDb file, and the compounds.dat of LycoCyc has names in HTML encoding, such as:
<i>D</i>-glycerate
However, the BridgeDb will have names without HTML, e.g. with UTF-8, though I would be happy to have the italics just removed. Is there a Java library that can convert a HTML string like that given above into a non-HTML string, for example in ASCII or even UTF-8 for some superscripted and subscripted digits?
What you are looking for are tools that implement the functionality called "strip html tags". This can be done with regular expressions, for example with sed
sed 's/<[^>]*>//g' index.html | more
or with various libraries like so:
http://stackoverflow.com/questions/753052/strip-html-from-strings-in-python
now moving that into superscript/subscript will require a custom HTML parsing and formatting.
Actually, this does not take care of HTML entities, like α ... other than that, I was hoping for a Java library, though I obviously can do regex's there too...
I found Jsoup that may serve my needs, or at least some. The library is small, and the Java code simple (or Groovy in this snippet):
println "val: " + value
value = Jsoup.parseBodyFragment(value).text()
println "val: " + value
This takes care of removing the HTML tags and the decoding of the HTML entities, but not the super/subscripting of digits. Example output:
val: trans-Δ<SUP>2</SUP>, cis-Δ<SUP>4</SUP>-decadienoyl-CoA
val: trans-Δ2, cis-Δ4-decadienoyl-CoA
I welcome other answers very much, particularly if they are smart about sub- and superscript!
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using xslt ?.
a possibility...
forget it , I thought you only wanted to grab the HTML pages.