Parsing with ruby - ruby

Question

I am new to ruby and I have a school project were I am parsing a xml file and need to get data after certain tags. I can only use core ruby. No gems
pFile = File.open("myfile.mzML", "r")
regmsLvl = "ms level\" value=\""
pFile.each_line { |line|
scn = line.scan(/#{regmsLvl}(\d)/)
#what I want to do but doesn't work
if scn == 1
puts("Got it!")
end
#what I have to do to compare if == 1
if scn != nil
scn.each do |val|
if val[0].to_i == 1
puts("Got it!")
end
end
end
}
# a sample line that I am parsing is:
<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
This seems silly.
line.scans out put makes scn a 2d array. How can I just have it be a string that gets overridden each pass. Or how should I change this whole thing. Any suggestions are appreciated.
puts(scn) prints out the 1 but if I do scn == 1 or scn.to_i == 1 it never gets into the if. I have tried scn.pop and scn.pop.pop
I have added a section to show what I am trying to do now.
I need to check the ms level: if 1 then get scan start time and then the binary. This is the code that I am now working with.
xmlfile = File.new("afile.mzML")
xmldoc = Document.new(xmlfile)
root = xmldoc.root
puts "Root element : " + root.attributes["xmlns"]
xmldoc.elements.each("mzML/run/spectrumList/spectrum/cvParam"){
|e| if e.attributes["value"].to_i ==1
# Now I need to get start time: #
["mzML/run/spectrumList/spectrum/cvParam/scanList/scan/value"]
# and then
["mzML/run/spectrumList/spectrum/cvParam/binaryDataArrayList/binaryDataArray/binary"]
end
}
<run id="ru_0" defaultInstrumentConfigurationRef="ic_0" sampleRef="sa_0" defaultSourceFileRef="sf_ru_0">
<spectrumList count="3310" defaultDataProcessingRef="dp_sp_0">
<spectrum id="scan=8839" index="0" defaultArrayLength="171" dataProcessingRef="dp_sp_0">
<cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />
<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
<cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
<scanList count="1">
<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
<scan>
<cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="5429.47" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
</scan>
</scanList>
<binaryDataArrayList count="2">
<binaryDataArray encodedLength="1824">
<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
<binary>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</binary>
</binaryDataArray>

Answer 1

I think you were pretty close. Assuming you can use that REXML library (which looks like it's part of the core ruby library) you should be able to do this
require 'rexml/document'
xmlfile = File.new("afile.mzML")
xmldoc = REXML::Document.new(xmlfile)
root = xmldoc.root
start_time = nil
binary = nil
# get the ms level
ms_level = root.elements["spectrumList/spectrum/cvParam[#name='ms level']"].attributes["value"].to_i
if ms_level == 1
# get the scan start time
start_time = root.elements["spectrumList/spectrum/scanList/scan/cvParam[#name='scan start time']"].attributes["value"]
# get the binary
binary = root.elements["spectrumList/spectrum/binaryDataArrayList/binaryDataArray/binary"].text
end
p start_time # => "5429.47"
p binary # => that crazy long binary
This REXML tutorial is helpful: http://www.germane-software.com/software/rexml/docs/tutorial.html
Note, I made a few assumptions, like the elements would always exist, the ms level was always an int, the file structure is always the same. Those assumptions may not be true in your situation but this should be a start.