QCDatabase/RunParametersParser.py at master · smrey/QCDatabase · GitHub

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'''
Created on 3 Nov 2015

@author: Sara
'''
class RunParametersParser(object):
    '''
    A series of methods to parse the runParameters file generated by Illumina sequencing instruments
    '''
    def __init__(self,filename): #,identifier
        '''
        In this method initial values for the internal data are created. The instance variables.
        This is within the namespace of the class.
        '''
        #RunParameters
        import xml.etree.ElementTree as ET
        tree = ET.parse(filename)
        root = tree.getroot()
        self.tree = tree
        self.root = root
        #self.locate = identifier

    def retrieveRPData(self,identifier):
        #print self.locate
        return (self.root.find(identifier).text)

    def retrieveNestedRPData(self,outer_identifier,identifier):
        #print self.locate
        #Sometimes there is no serial number for the flow cell (strange) in the runparameters file- causes an error, need to handle this
        #Return an empty string where there is no data in  the runparameters file
        try:
            return (self.root.find(outer_identifier).find(identifier).text)
        except:
            return ' '

    def returnElementInfo(self,identifier,subelm1,subelm2,subelm3):
        '''
        This is a bit specialised for the Reads circumstance, because of the Y,N becoming 1,0 for the database.
        Could fix later if required
        '''
        ident = self.root.find(identifier)
        ident_list = []
        for subelement in ident:
            ident_list.append(subelement.attrib.get(subelm1))
            if (subelement.attrib.get(subelm2)) == 'Y':
                ident_list.append('1')
            elif (subelement.attrib.get(subelm2)) == 'N':
                ident_list.append('0')
            else:
                raise Exception("Problem with subelement2")
            ident_list.append(subelement.attrib.get(subelm3))
        return ident_list

    def getNumSubelements(self,identifier):
        reads = self.root.find(identifier)
        return len(reads) #No need to iterate through as this works just as well