def testEmptyGSuite(self):
gSuite = GSuite()
self.assertEqual('unknown', gSuite.location)
self.assertEqual('unknown', gSuite.fileFormat)
self.assertEqual('unknown', gSuite.trackType)
self.assertEqual('unknown', gSuite.genome)
self.assertEqual([], gSuite.attributes)
self.assertEqual(False, gSuite.isPreprocessed())
self.assertEqual(False, gSuite.hasCustomTitles())
self.assertEqual(0, gSuite.numTracks())
self.assertEqual(0, len(list(gSuite.allTracks())))
self.assertEqual(0, len(list(gSuite.allTrackTitles())))
self.assertEqual(0, len(list(gSuite.allTrackTypes())))
def testAddGSuiteTracks(self):
gSuite = GSuite()
gSuite.setGenomeOfAllTracks('hg18')
self.assertEqual('unknown', gSuite.genome)
gSuite.addTrack(GSuiteTrack('ftp://server.somewhere.com/path/to/file1.bed',
title='Track1', \
attributes=OrderedDict([('cell', 'k562'),
('antibody', 'cMyb')])))
gSuite.addTrack(GSuiteTrack('http://server.other.com/path/to/file2.bed',
title='Track2', \
attributes=OrderedDict([('cell', 'GM12878'),
('antibody', 'cMyc')])))
gSuite.addTrack(
GSuiteTrack('https://server.other.com/path/to/file3.bed',
attributes=OrderedDict([('cell', 'GM12878'),
('antibody', 'cMyb')])))
gSuite.addTrack(
GSuiteTrack(
'rsync://server.other.com/other/path/to/file3.bed;bed9',
attributes=OrderedDict([('cell', 'NHFL')])))
gSuite.setGenomeOfAllTracks('hg18')
self.assertEqual('remote', gSuite.location)
self.assertEqual('primary', gSuite.fileFormat)
self.assertEqual('unknown', gSuite.trackType)
self.assertEqual('hg18', gSuite.genome)
self.assertEqual(['cell', 'antibody'], gSuite.attributes)
self.assertEqual(False, gSuite.isPreprocessed())
self.assertEqual(True, gSuite.hasCustomTitles())
self.assertEqual(4, gSuite.numTracks())
self.assertEqual(['hg18'] * 4, [x.genome for x in gSuite.allTracks()])
self.assertEqual(['Track1', 'Track2', 'file3.bed', 'file3.bed (2)'],
gSuite.allTrackTitles())
self.assertEqual(['unknown'], gSuite.allTrackTypes())
gSuite.addTrack(
GSuiteTrack('hb:/track/name/hierarchy',
title='Track1',
genome='hg19',
trackType='segments'))
self.assertEqual('multiple', gSuite.genome)
gSuite.addTrack(GSuiteTrack('galaxy:/ad123dd12fg;btrack?track=track:name',
title='Track2', \
attributes=OrderedDict([('cell', 'k562'),
('antibody', 'cMyb')])))
gSuite.addTrack(GSuiteTrack('file:/path/to/file.btrack?track=track:name',
title='Track2', \
attributes=OrderedDict([('antibody', 'cMyb'),
('extra', 'yes')])))
self.assertEqual('multiple', gSuite.location)
self.assertEqual('multiple', gSuite.fileFormat)
self.assertEqual('unknown', gSuite.trackType)
self.assertEqual('unknown', gSuite.genome)
self.assertEqual(['cell', 'antibody', 'extra'], gSuite.attributes)
self.assertEqual(False, gSuite.isPreprocessed())
self.assertEqual(True, gSuite.hasCustomTitles())
self.assertEqual(7, gSuite.numTracks())
self.assertEqual(['hg18'] * 4 + ['hg19'] + ['unknown'] * 2,
[x.genome for x in gSuite.allTracks()])
self.assertEqual(['Track1', 'Track2', 'file3.bed', 'file3.bed (2)', \
'Track1 (2)', 'Track2 (2)', 'Track2 (3)'],
gSuite.allTrackTitles())
self.assertEqual(['segments', 'unknown'], gSuite.allTrackTypes())
self.assertRaises(
InvalidFormatError,
gSuite.addTrack,
GSuiteTrack('https://server.third.com/path/to/file3.bed'),
allowDuplicateTitles=False)
attributes=OrderedDict([('a', 'yes'), ('b', 'no')])))
uri2 = HbGSuiteTrack.generateURI(
trackName=['Genes and gene subsets', 'Genes', 'Refseq'])
gSuite.addTrack(
GSuiteTrack(uri2, attributes=OrderedDict([('b', 'no'), ('c', 'yes')])))
gSuite.setGenomeOfAllTracks('hg19')
contents = GSuiteComposer.composeToString(gSuite)
print 'GSuite file contents'
print '--------------------'
print contents
gSuite2 = GSuiteParser.parseFromString(contents)
print 'Various ways of direct access'
print '-----------------------------'
print "genome=%s, location=%s, file format=%s, track type=%s, attributes=%s" % \
(gSuite.genome, gSuite.location, gSuite.fileFormat, gSuite.trackType, gSuite.attributes)
for track in gSuite2.allTracks():
print "uri=%s, path=%s, trackName=%s" % (track.uri, track.path,
track.trackName)
print "netloc=" + gSuite2.getTrackFromTitle('Track1').netloc
tracks = list(gSuite.allTracks())
print "b=" + tracks[1].attributes['b']
