Example #1
0
 def test_addFilters(self):
     ds1 = DataSet()
     filt = Filters()
     filt.addRequirement(rq=[('>', '0.85')])
     ds1.addFilters(filt)
     self.assertEquals(str(ds1.filters), '( rq > 0.85 )')
     # Or added from a source XML
     ds2 = DataSet(data.getXml(16))
     self.assertTrue(str(ds2.filters).startswith('( rname = E.faecalis'))
 def test_addFilters(self):
     ds1 = DataSet()
     filt = Filters()
     filt.addRequirement(rq=[('>', '0.85')])
     ds1.addFilters(filt)
     assert str(ds1.filters) == '( rq > 0.85 )'
     # Or added from a source XML
     ds2 = DataSet(data.getXml(15))
     assert str(ds2.filters).startswith('( rname = E.faecalis')
Example #3
0
 def test_setFilters(self):
     ds1 = DataSet()
     filt = Filters()
     filt.addRequirement(rq=[('>', '0.85')])
     ds1.addFilters(filt)
     self.assertEquals(str(ds1.filters), '( rq > 0.85 )')
     # Or added from a source XML
     ds2 = DataSet()
     ds2.filters = ds1.filters
     self.assertEquals(str(ds2.filters), '( rq > 0.85 )')
Example #4
0
 def test_addFilters(self):
     ds1 = DataSet()
     filt = Filters()
     filt.addRequirement(rq=[('>', '0.85')])
     ds1.addFilters(filt)
     self.assertEquals(str(ds1.filters), '( rq > 0.85 )')
     # Or added from a source XML
     ds2 = DataSet(data.getXml(16))
     self.assertTrue(str(ds2.filters).startswith(
         '( rname = E.faecalis'))
 def test_setFilters(self):
     ds1 = DataSet()
     filt = Filters()
     filt.addRequirement(rq=[('>', '0.85')])
     ds1.addFilters(filt)
     self.assertEquals(str(ds1.filters), '( rq > 0.85 )')
     # Or added from a source XML
     ds2 = DataSet()
     ds2.filters = ds1.filters
     self.assertEquals(str(ds2.filters), '( rq > 0.85 )')
Example #6
0
 def test_filter_reference_contigs(self):
     ds2 = ReferenceSet(data.getRef())
     self.assertEqual(len(list(ds2.refNames)), 59)
     filt = Filters()
     filt.addRequirement(id=[('==', 'E.faecalis.1')])
     ds2.addFilters(filt)
     self.assertEqual(str(ds2.filters), "( id == E.faecalis.1 )")
     self.assertEqual(len(ds2.refNames), 1)
     self.assertEqual(len(list(ds2.records)), 1)
     ds2.disableFilters()
     self.assertEqual(len(list(ds2.refNames)), 59)
     self.assertEqual(len(list(ds2.records)), 59)
     ds2.enableFilters()
     self.assertEqual(len(list(ds2.refNames)), 1)
     self.assertEqual(len(list(ds2.records)), 1)
Example #7
0
def _parseXmlFilters(element):
    """Pull filters from XML file, put them in a list of dictionaries, where
    each dictionary contains a representation of a Filter tag: key, value pairs
    with parameter names and value expressions.

    Doctest:
        >>> import xml.etree.ElementTree as ET
        >>> import pbcore.data.datasets as data
        >>> tree = ET.parse(data.getXml(no=8).split(':')[1])
        >>> root = tree.getroot()
        >>> filters = root[1]
        >>> str(_parseXmlFilters(filters))
        '( rq > 0.75 ) OR ( qname == 100/0/0_100 )'
    """
    """
    namer = functools.partial(_namespaceTag, XMLNS)
    result = []
    for filtTag in filters:
        #filt = Filter()
        filt = {}
        # This is essentially to skip the <Parameters> level
        for child in filtTag:
            if child.tag == namer('Parameters'):
                for param in child:
                    filt[param.attrib['Name'].lower()] = param.attrib['Value']
        result.append(filt)
    return result
    """
    return Filters(_eleToDictList(element))
Example #8
0
 def test_filter_reference_contigs(self):
     ds2 = ReferenceSet(data.getRef())
     self.assertEqual(len(list(ds2.refNames)), 59)
     filt = Filters()
     filt.addRequirement(id=[('==', 'E.faecalis.1')])
     ds2.addFilters(filt)
     self.assertEqual(str(ds2.filters),
                      "( id == E.faecalis.1 )")
     self.assertEqual(len(ds2.refNames), 1)
     self.assertEqual(len(list(ds2.records)), 1)
     ds2.disableFilters()
     self.assertEqual(len(list(ds2.refNames)), 59)
     self.assertEqual(len(list(ds2.records)), 59)
     ds2.enableFilters()
     self.assertEqual(len(list(ds2.refNames)), 1)
     self.assertEqual(len(list(ds2.records)), 1)
Example #9
0
def filter_options(parser):
    pbiFilterOptions = set(Filters()._pbiMappedVecAccMap().keys())
    bamFilterOptions = set(Filters()._bamAccMap.keys())
    parser.description = ('Add filters to an XML file. Suggested fields: '
                          '{f}. More expensive fields: {b}'.format(
                              f=sorted(list(pbiFilterOptions)),
                              b=sorted(
                                  list(bamFilterOptions - pbiFilterOptions))))
    #parser.add_argument("infile", type=validate_file,
    parser.add_argument("infile", type=str, help="The xml file to filter")
    parser.add_argument("outfile", type=str, help="The resulting xml file")
    parser.add_argument("filters",
                        type=str,
                        nargs='+',
                        help="The values and thresholds to filter (e.g. "
                        "'rq>0.85')")
    parser.set_defaults(func=filterXml)
 def test_filter_reference_contigs(self):
     ds2 = ReferenceSet(data.getRef())
     assert len(list(ds2.refNames)) == 59
     assert len(list(ds2.records)) == len(ds2.index)
     filt = Filters()
     filt.addRequirement(id=[('==', 'E.faecalis.1')])
     ds2.addFilters(filt)
     assert str(ds2.filters) == "( id == E.faecalis.1 )"
     assert len(ds2.refNames) == 1
     assert len(list(ds2.records)) == 1
     assert len(list(ds2.records)) == len(ds2.index)
     ds2.disableFilters()
     assert len(list(ds2.refNames)) == 59
     assert len(list(ds2.records)) == 59
     assert len(list(ds2.records)) == len(ds2.index)
     ds2.enableFilters()
     assert len(list(ds2.refNames)) == 1
     assert len(list(ds2.records)) == 1
     assert len(list(ds2.records)) == len(ds2.index)
Example #11
0
def filter_options(parser):
    pbiFilterOptions = set(Filters()._pbiMappedVecAccMap().keys())
    bamFilterOptions = set(Filters()._bamAccMap.keys())
    parser.description = ('Add filters to an XML file. Suggested fields: '
                          '{f}. More expensive fields: {b}.\nMultiple filters '
                          'of different names will be ANDed together, '
                          'multiple filters of the same name will be ORed '
                          'together, duplicating existing requirements'.format(
                              f=sorted(list(pbiFilterOptions)),
                              b=sorted(
                                  list(bamFilterOptions - pbiFilterOptions))))
    # parser.add_argument("infile", type=validate_file,
    parser.add_argument("infile", type=str, help="The XML file to filter")
    parser.add_argument("outfile",
                        type=str,
                        help="The resulting DataSet XML file")
    parser.add_argument("filters",
                        type=str,
                        nargs='+',
                        help=("The parameters, operators and values to filter "
                              "(e.g. 'rq>0.85')"))
    parser.set_defaults(func=filterXml)
Example #12
0
    def test_reads_in_contig(self):
        log.info("Testing reads in contigs")
        ds = DataSet(data.getXml(8))
        dss = ds.split(contigs=True)
        self.assertEqual(len(dss), 12)
        efaec1TimesFound = 0
        efaec1TotFound = 0
        efaec2TimesFound = 0
        efaec2TotFound = 0
        for ds in dss:
            ef1 = len(list(ds.readsInReference('E.faecalis.1')))
            ef2 = len(list(ds.readsInReference('E.faecalis.2')))
            if ef1:
                efaec1TimesFound += 1
                efaec1TotFound += ef1
            if ef2:
                efaec2TimesFound += 1
                efaec2TotFound += ef2
        self.assertEqual(efaec1TimesFound, 1)
        self.assertEqual(efaec1TotFound, 20)
        self.assertEqual(efaec2TimesFound, 1)
        self.assertEqual(efaec2TotFound, 3)

        ds = DataSet(data.getXml(8))
        filt = Filters()
        filt.addRequirement(length=[('>', '100')])
        ds.addFilters(filt)
        dss = ds.split(contigs=True)
        self.assertEqual(len(dss), 12)
        efaec1TimesFound = 0
        efaec1TotFound = 0
        efaec2TimesFound = 0
        efaec2TotFound = 0
        for ds in dss:
            ef1 = len(list(ds.readsInReference('E.faecalis.1')))
            ef2 = len(list(ds.readsInReference('E.faecalis.2')))
            if ef1:
                efaec1TimesFound += 1
                efaec1TotFound += ef1
            if ef2:
                efaec2TimesFound += 1
                efaec2TotFound += ef2
        self.assertEqual(efaec1TimesFound, 1)
        self.assertEqual(efaec1TotFound, 20)
        self.assertEqual(efaec2TimesFound, 1)
        self.assertEqual(efaec2TotFound, 3)

        ds = DataSet(data.getXml(8))
        filt = Filters()
        filt.addRequirement(length=[('>', '1000')])
        ds.addFilters(filt)
        dss = ds.split(contigs=True)
        self.assertEqual(len(dss), 9)
        efaec1TimesFound = 0
        efaec1TotFound = 0
        efaec2TimesFound = 0
        efaec2TotFound = 0
        for ds in dss:
            ef1 = len(list(ds.readsInReference('E.faecalis.1')))
            ef2 = len(list(ds.readsInReference('E.faecalis.2')))
            if ef1:
                efaec1TimesFound += 1
                efaec1TotFound += ef1
            if ef2:
                efaec2TimesFound += 1
                efaec2TotFound += ef2
        self.assertEqual(efaec1TimesFound, 1)
        self.assertEqual(efaec1TotFound, 20)
        self.assertEqual(efaec2TimesFound, 1)
        self.assertEqual(efaec2TotFound, 1)
Example #13
0
def _parseXmlFilters(element):
    """Pull filters from XML file, put them in a list of dictionaries, where
    each dictionary contains a representation of a Filter tag: key, value pairs
    with parameter names and value expressions.
    """
    return Filters(_eleToDictList(element))
Example #14
0
    def test_reads_in_contig(self):
        log.info("Testing reads in contigs")
        ds = DataSet(data.getXml(8))
        dss = ds.split(contigs=True)
        self.assertEqual(len(dss), 12)
        efaec1TimesFound = 0
        efaec1TotFound = 0
        efaec2TimesFound = 0
        efaec2TotFound = 0
        for ds in dss:
            ef1 = len(list(ds.readsInReference('E.faecalis.1')))
            ef2 = len(list(ds.readsInReference('E.faecalis.2')))
            if ef1:
                efaec1TimesFound += 1
                efaec1TotFound += ef1
            if ef2:
                efaec2TimesFound += 1
                efaec2TotFound += ef2
        self.assertEqual(efaec1TimesFound, 1)
        self.assertEqual(efaec1TotFound, 20)
        self.assertEqual(efaec2TimesFound, 1)
        self.assertEqual(efaec2TotFound, 3)

        ds = DataSet(data.getXml(8))
        filt = Filters()
        filt.addRequirement(length=[('>', '100')])
        ds.addFilters(filt)
        dss = ds.split(contigs=True)
        self.assertEqual(len(dss), 12)
        efaec1TimesFound = 0
        efaec1TotFound = 0
        efaec2TimesFound = 0
        efaec2TotFound = 0
        for ds in dss:
            ef1 = len(list(ds.readsInReference('E.faecalis.1')))
            ef2 = len(list(ds.readsInReference('E.faecalis.2')))
            if ef1:
                efaec1TimesFound += 1
                efaec1TotFound += ef1
            if ef2:
                efaec2TimesFound += 1
                efaec2TotFound += ef2
        self.assertEqual(efaec1TimesFound, 1)
        self.assertEqual(efaec1TotFound, 20)
        self.assertEqual(efaec2TimesFound, 1)
        self.assertEqual(efaec2TotFound, 3)

        ds = DataSet(data.getXml(8))
        filt = Filters()
        filt.addRequirement(length=[('>', '1000')])
        ds.addFilters(filt)
        dss = ds.split(contigs=True)
        self.assertEqual(len(dss), 9)
        efaec1TimesFound = 0
        efaec1TotFound = 0
        efaec2TimesFound = 0
        efaec2TotFound = 0
        for ds in dss:
            ef1 = len(list(ds.readsInReference('E.faecalis.1')))
            ef2 = len(list(ds.readsInReference('E.faecalis.2')))
            if ef1:
                efaec1TimesFound += 1
                efaec1TotFound += ef1
            if ef2:
                efaec2TimesFound += 1
                efaec2TotFound += ef2
        self.assertEqual(efaec1TimesFound, 1)
        self.assertEqual(efaec1TotFound, 20)
        self.assertEqual(efaec2TimesFound, 1)
        self.assertEqual(efaec2TotFound, 1)