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#!/bin/env groovy
/*
* Copyright (C) 2009-2011 Institute for Computational Biomedicine,
* Weill Medical College of Cornell University
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
//
// When files are sequenced, the directory containing the sequences (s_#_sequence.txt.gz)
// contains a file "Summary.xml". This will parse that file and display the
// sampleId's and sequenceId's within the summary file.
//
// As command line arguments, this script takes one or more summary files
// or directories. Any directories that are provided will be used to find
// the file Summary.xml.
//
import org.xml.sax.SAXParseException
for (arg in args) {
def file = new File(arg)
if (!file.exists()) {
println "Argument ${arg} doesn't represent either a file or a directory"
continue
}
if (file.isDirectory()) {
file = new File(file, "Summary.xml")
}
parseXmlSummaryFile(file)
}
def parseXmlSummaryFile(File summaryFile) {
if (!summaryFile.exists()) {
println "Could not find file to parse: ${summaryFile.toString()}"
return
}
println "Summary file: ${summaryFile.toString()}"
try {
def xml = new XmlParser().parse(summaryFile)
def lanes = xml.Samples.Lane
for (lane in lanes) {
String laneNumber = lane.laneNumber.text().trim()
String sampleId = lane.sampleId.text().trim()
println " sampldId = ${sampleId}, laneNumber=${laneNumber}"
}
} catch (SAXParseException e) {
println "WARN: Couldn't parse ${summaryFile.toString()}"
}
}
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