def testComposeLocalUrlGenomeAttributesNonAscii(self):
gSuite = GSuite()
gSuite.addTrack(
GSuiteTrack('galaxy:/12345abc',
genome=u'hg18ø',
attributes=OrderedDict([('one', 'yes')])))
gSuite.addTrack(
GSuiteTrack('file:/path/to/file2',
genome='hg19',
attributes=OrderedDict([('two', u'nø')])))
gSuite.addTrack(
GSuiteTrack(
HbGSuiteTrack.generateURI(trackName=[u'track', u'nøme']),
genome='hg38',
attributes=OrderedDict([('two', 'yes')])))
gSuite.setCustomHeader('my header', u'bø!')
output = GSuiteComposer.composeToString(gSuite)
targetOutput = \
'##location: local\n' \
'##file format: unknown\n' \
'##track type: unknown\n' \
'##genome: multiple\n' \
'##my header: b%C3%B8!\n' \
'###uri\ttitle\tfile_format\tgenome\tone\ttwo\n' \
'galaxy:/12345abc\t12345abc\tunknown\thg18%C3%B8\tyes\t.\n' \
'file:/path/to/file2\tfile2\tunknown\thg19\t.\tn%C3%B8\n' \
'hb:/track/n%C3%B8me\tn%C3%B8me\tpreprocessed\thg38\t.\tyes\n'
self.assertEquals(targetOutput, output)
def testEmptyCompose(self):
gSuite = GSuite()
output = GSuiteComposer.composeToString(gSuite)
targetOutput = \
'##location: unknown\n' \
'##file format: unknown\n' \
'##track type: unknown\n' \
'##genome: unknown\n'
self.assertEquals(targetOutput, output)
def testFullCompose(self):
gSuite = GSuite()
gSuite.addTrack(
GSuiteTrack('ftp://server.somewhere.com/path/to/file1.bed',
title='Track',
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/path/to/file4;wig',
title='Track4',
attributes=OrderedDict([('cell', 'NHFL')])))
gSuite.addTrack(GSuiteTrack('hb:/track/name/hierarchy', title='Track'))
gSuite.addTrack(
GSuiteTrack('galaxy:/ad123dd12fg;btrack?track=track:name',
title='Track',
attributes=OrderedDict([('cell', 'k562'),
('antibody', 'cMyb')])))
gSuite.addTrack(
GSuiteTrack('file:/path/to/file.btrack?track=track:name',
title='Track name7',
attributes=OrderedDict([('antibody', 'cMyb'),
('extra', 'yes')])))
gSuite.setGenomeOfAllTracks('hg18')
gSuite.setCustomHeader('My header', 'Some value')
output = GSuiteComposer.composeToString(gSuite)
targetOutput = \
'##location: multiple\n' \
'##file format: multiple\n' \
'##track type: unknown\n' \
'##genome: hg18\n' \
'##my header: Some value\n' \
'###uri\ttitle\tfile_format\tcell\tantibody\textra\n' \
'ftp://server.somewhere.com/path/to/file1.bed\tTrack\tprimary\tk562\tcMyb\t.\n' \
'http://server.other.com/path/to/file2.bed\tTrack2\tprimary\tGM12878\tcMyc\t.\n' \
'https://server.other.com/path/to/file3.bed\tfile3.bed\tprimary\tGM12878\tcMyb\t.\n' \
'rsync://server.other.com/path/to/file4;wig\tTrack4\tprimary\tNHFL\t.\t.\n' \
'hb:/track/name/hierarchy\tTrack (2)\tpreprocessed\t.\t.\t.\n' \
'galaxy:/ad123dd12fg;btrack?track=track%3Aname\tTrack (3)\tpreprocessed\tk562\tcMyb\t.\n' \
'file:/path/to/file.btrack?track=track%3Aname\tTrack name7\tpreprocessed\t.\tcMyb\tyes\n'
self.assertEquals(targetOutput, output)
def testComposeRemoteOnlyUrl(self):
gSuite = GSuite()
gSuite.addTrack(
GSuiteTrack('ftp://server.somewhere.com/path/to/file1'))
gSuite.addTrack(GSuiteTrack('http://server.other.com/path/to/file2'))
output = GSuiteComposer.composeToString(gSuite)
targetOutput = \
'##location: remote\n' \
'##file format: unknown\n' \
'##track type: unknown\n' \
'##genome: unknown\n' \
'###uri\ttitle\n' \
'ftp://server.somewhere.com/path/to/file1\tfile1\n' \
'http://server.other.com/path/to/file2\tfile2\n'
self.assertEquals(targetOutput, output)
def testParseAndCompose(self):
inputContents = \
'##location: multiple\n' \
'##file format: multiple\n' \
'##track type: unknown\n' \
'##genome: hg18\n' \
'###uri\ttitle\tfile_format\tcell\tantibody\textra\n' \
'ftp://server.somewhere.com/path/to/file1.bed\tTrack1\tprimary\tk562\tcMyb\t.\n' \
'http://server.other.com/path/to/file2.bed\tTrack2\tprimary\tGM12878\tcMyc\t.\n' \
'https://server.other.com/path/to/file3.bed\tfile3.bed\tprimary\tGM12878\tcMyb\t.\n' \
'rsync://server.other.com/path/to/file4;wig\tTrack4\tprimary\tNHFL\t.\t.\n' \
'hb:/track/name/hierarchy\tTrack5\tpreprocessed\t.\t.\t.\n' \
'galaxy:/ad123dd12fg;btrack?track=track%3Aname\tTrack6\tpreprocessed\tk562\tcMyb\t.\n' \
'file:/path/to/file.btrack?track=track%3Aname\tTrack name7\tpreprocessed\t.\tcMyb\tyes\n'
gSuite = GSuiteParser.parseLines(inputContents.split('\n'))
outputContents = GSuiteComposer.composeToString(gSuite)
self.assertEquals(inputContents, outputContents)
def testComposeUrlTitleLocationTrackType(self):
gSuite = GSuite()
gSuite.addTrack(
GSuiteTrack('ftp://server.somewhere.com/path/to/file1',
title='Track1',
trackType='points'))
gSuite.addTrack(
GSuiteTrack('file:/path/to/file2', trackType='segments'))
output = GSuiteComposer.composeToString(gSuite)
targetOutput = \
'##location: multiple\n' \
'##file format: unknown\n' \
'##track type: multiple\n' \
'##genome: unknown\n' \
'###uri\ttitle\ttrack_type\n' \
'ftp://server.somewhere.com/path/to/file1\tTrack1\tpoints\n' \
'file:/path/to/file2\tfile2\tsegments\n'
self.assertEquals(targetOutput, output)
def testComposeRemoteUrlGenomeFileFormat(self):
gSuite = GSuite()
gSuite.addTrack(
GSuiteTrack('ftp://server.somewhere.com/path/to/file1.bed',
genome='hg18'))
gSuite.addTrack(
GSuiteTrack('http://server.other.com/path/to/file2',
genome='hg18'))
output = GSuiteComposer.composeToString(gSuite)
targetOutput = \
'##location: remote\n' \
'##file format: unknown\n' \
'##track type: unknown\n' \
'##genome: hg18\n' \
'###uri\ttitle\tfile_format\n' \
'ftp://server.somewhere.com/path/to/file1.bed\tfile1.bed\tprimary\n' \
'http://server.other.com/path/to/file2\tfile2\tunknown\n'
self.assertEquals(targetOutput, output)
def testComposeLocalUrlGenomeAttributes(self):
gSuite = GSuite()
gSuite.addTrack(
GSuiteTrack('galaxy:/12345abc',
genome='hg18',
attributes=OrderedDict([('one', 'yes')])))
gSuite.addTrack(
GSuiteTrack('file:/path/to/file2',
genome='hg19',
attributes=OrderedDict([('two', 'no')])))
output = GSuiteComposer.composeToString(gSuite)
targetOutput = \
'##location: local\n' \
'##file format: unknown\n' \
'##track type: unknown\n' \
'##genome: multiple\n' \
'###uri\ttitle\tgenome\tone\ttwo\n' \
'galaxy:/12345abc\t12345abc\thg18\tyes\t.\n' \
'file:/path/to/file2\tfile2\thg19\t.\tno\n'
self.assertEquals(targetOutput, output)
def __str__(self):
import gold.gsuite.GSuiteComposer as GSuiteComposer
return GSuiteComposer.composeToString(self)
gSuite = GSuite()
uri1 = FtpGSuiteTrack.generateURI(netloc='server.com', path='file.bed')
gSuite.addTrack(
GSuiteTrack(uri1,
title='Track1',
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)