def test_readVer8Project(self):
"""
Tests reading a version 0.8 project file and conversion to 1.0.0
format.
"""
self.proj.loadProjectFile('test_data/test_project-0.8.str')
# Test if the project properties are correct.
self.assertFalse(self.proj.isProjectEmpty())
self.assertEqual(self.proj.getFwdTraceSearchStr(), '_F_')
self.assertEqual(self.proj.getRevTraceSearchStr(), '_R_')
self.assertEqual(self.proj.getTraceFileDir(), 'tracedir')
self.assertEqual(self.proj.getAbsTraceFileDir(),
os.path.join(os.getcwd(), 'test_data/tracedir'))
self.assertEqual(getDefaultFont().to_string(),
self.proj.getFont().to_string())
# Test if the consensus settings are correct.
csettings = self.proj.getConsensSeqSettings()
self.assertEqual(csettings.getMinConfScore(), 20)
self.assertEqual(csettings.getConsensusAlgorithm(), 'legacy')
self.assertFalse(csettings.getTrimConsensus())
self.assertFalse(csettings.getTrimPrimers())
self.assertEqual(csettings.getPrimerMatchThreshold(), 0.8)
self.assertEqual(csettings.getForwardPrimer(), '')
self.assertEqual(csettings.getReversePrimer(), '')
self.assertFalse(csettings.getTrimEndGaps())
self.assertFalse(csettings.getDoQualityTrim())
self.assertEqual(csettings.getQualityTrimParams(), (10, 6))
self.proj.setTraceFileDir('.')
for fname in self.tracefiles:
self.assertTrue(self.proj.isFileInProject('test_data/' + fname))
self._checkProjectItems(self.proj, 'fwd2.ztr', 'rev2.ztr')
def convertOldProjectFormat(self):
"""
Converts an older project format to the current project format.
"""
if self.proj_data['formatversion'] == '0.8':
self.convertSettings8To9()
self.proj_data['formatversion'] = '0.9'
if self.proj_data['formatversion'] == '0.9':
fontstr = getDefaultFont().to_string()
self.proj_data['properties']['default_font'] = fontstr
self.proj_data['formatversion'] = CURRENT_VERSION
def test_clearProject(self):
# First, set all of the various project settings.
self.proj.addFiles(self.tracefiles)
self.proj.setFwdTraceSearchStr('_F_')
self.proj.setFwdTraceSearchStr('_R_')
self.proj.setTraceFileDir('tracedir')
newfont = getDefaultFont()
default_font_str = newfont.to_string()
newfont.set_size(newfont.get_size() + 1)
self.proj.setFont(newfont)
self.assertNotEqual(default_font_str, self.proj.getFont().to_string())
csettings = self.proj.getConsensSeqSettings()
csettings.setMinConfScore(20)
csettings.setConsensusAlgorithm('legacy')
csettings.setTrimConsensus(False)
csettings.setTrimPrimers(True)
csettings.setPrimerMatchThreshold(0.2)
csettings.setForwardPrimer('AAAT')
csettings.setReversePrimer('AAAT')
csettings.setTrimEndGaps(False)
csettings.setDoQualityTrim(False)
csettings.setQualityTrimParams(20, 18)
self.proj.clearProject()
# Now make sure the project is empty and all settings have default
# values.
self.assertTrue(self.proj.isProjectEmpty())
for file in self.tracefiles:
self.assertFalse(self.proj.isFileInProject(file))
self.assertEqual(self.proj.getFwdTraceSearchStr(), '_F')
self.assertEqual(self.proj.getRevTraceSearchStr(), '_R')
self.assertEqual(self.proj.getTraceFileDir(), '.')
self.assertEqual(self.proj.getAbsTraceFileDir(), os.getcwd())
self.assertEqual(default_font_str, self.proj.getFont().to_string())
csettings = self.proj.getConsensSeqSettings()
self.assertEqual(csettings.getMinConfScore(), 30)
self.assertEqual(csettings.getConsensusAlgorithm(), 'Bayesian')
self.assertTrue(csettings.getTrimConsensus())
self.assertFalse(csettings.getTrimEndGaps())
self.assertFalse(csettings.getTrimPrimers())
self.assertEqual(csettings.getForwardPrimer(), '')
self.assertEqual(csettings.getReversePrimer(), '')
self.assertEqual(csettings.getPrimerMatchThreshold(), 0.8)
self.assertTrue(csettings.getDoQualityTrim())
self.assertEqual(csettings.getQualityTrimParams(), (10, 8))
def clearProject(self, notify=True):
# start numbering for node IDs at 0 by default
self.idnum = 0
self.project_file = ''
self.trace_file_dir = '.'
self.fwd_trace_searchstr = '_F'
self.rev_trace_searchstr = '_R'
self.default_font = getDefaultFont()
# Copy default consensus sequence settings rather than change
# references to a new settings object in case there are any active
# users of the existing settings object.
settings = ConsensSeqSettings()
self.consseqsettings.copyFrom(settings)
self.ts.clear()
self.num_files = 0
self.setSaveState(True)
if notify:
self.notifyObservers('project_cleared', ())
def test_readWriteProject(self):
# Write the test project file in a temporary directory.
tmpdir = tempfile.mkdtemp()
tmpfpath = os.path.join(tmpdir, self.filename)
self.proj.setProjectFileName(tmpfpath)
self.proj.addFiles(self.tracefiles)
self.proj.setFwdTraceSearchStr('_F_')
self.proj.setRevTraceSearchStr('_R_')
self.proj.setTraceFileDir('tracedir')
# Set a non-default font.
newfont = getDefaultFont()
newfont.set_size(newfont.get_size() + 1)
newfontstr = newfont.to_string()
self.assertNotEqual(newfontstr, self.proj.getFont().to_string())
self.proj.setFont(newfont)
# Set all consensus settings.
csettings = self.proj.getConsensSeqSettings()
csettings.setMinConfScore(20)
csettings.setConsensusAlgorithm('legacy')
csettings.setTrimConsensus(False)
csettings.setTrimPrimers(True)
csettings.setPrimerMatchThreshold(0.2)
csettings.setForwardPrimer('AAAT')
csettings.setReversePrimer('GGGC')
csettings.setTrimEndGaps(True)
csettings.setDoQualityTrim(False)
csettings.setQualityTrimParams(20, 18)
# Create an associative item.
a_item = self.proj.associateItems(
(self.proj.getItemById(2), self.proj.getItemById(3)), 'new item')
# Set some properties of the associative item and its children.
a_item.setNotes('sample notes')
a_item.setConsensusSequence('AATTAATTGGCC', 'AA TT AA TT GGCC')
a_item.setUseSequence(True)
child1 = a_item.getChildren()[0]
child2 = a_item.getChildren()[1]
child1name = child1.getName()
child2name = child2.getName()
child1.setConsensusSequence('CATCATGATCATTAGTAC',
'CATCATGATCAT TAGTAC')
child2.setIsReverse(True)
# Set sequences and notes for the remaining items.
# item 0: ''
# item 1: 'AT'
# item 3: 'ATATAT'
for (cnt, item) in enumerate(self.proj):
if item.isFile():
item.setConsensusSequence('AT' * cnt, 'AT' * cnt)
item.setNotes(str(cnt))
self.proj.saveProjectFile()
self.proj.clearProject()
self.proj.loadProjectFile(tmpfpath)
# Test if the project properties saved properly.
self.assertFalse(self.proj.isProjectEmpty())
self.assertEqual(self.proj.getFwdTraceSearchStr(), '_F_')
self.assertEqual(self.proj.getRevTraceSearchStr(), '_R_')
self.assertEqual(self.proj.getTraceFileDir(), 'tracedir')
self.assertEqual(self.proj.getAbsTraceFileDir(),
os.path.join(tmpdir, 'tracedir'))
self.assertEqual(newfontstr, self.proj.getFont().to_string())
# Test if the consensus settings saved properly.
csettings = self.proj.getConsensSeqSettings()
self.assertEqual(csettings.getMinConfScore(), 20)
self.assertEqual(csettings.getConsensusAlgorithm(), 'legacy')
self.assertFalse(csettings.getTrimConsensus())
self.assertTrue(csettings.getTrimPrimers())
self.assertEqual(csettings.getPrimerMatchThreshold(), 0.2)
self.assertEqual(csettings.getForwardPrimer(), 'AAAT')
self.assertEqual(csettings.getReversePrimer(), 'GGGC')
self.assertTrue(csettings.getTrimEndGaps())
self.assertFalse(csettings.getDoQualityTrim())
self.assertEqual(csettings.getQualityTrimParams(), (20, 18))
self.proj.setTraceFileDir('.')
for fname in self.tracefiles:
self.assertTrue(
self.proj.isFileInProject(os.path.join(tmpdir, fname)))
self._checkProjectItems(self.proj, child1name, child2name)
# Remove the temporary directory.
shutil.rmtree(tmpdir)
def __init__(self, sequencetrace):
self.min_height = 100
self.preferred_height = 200
self.drawingarea = Gtk.DrawingArea()
self.drawingarea.set_size_request(-1, self.min_height)
self.seqt = sequencetrace
# Initialize drawing settings.
self.tracecolors = {
'A': parseHTMLColorStr('#009000'), # green
'C': parseHTMLColorStr('#0000ff'), # blue
'G': parseHTMLColorStr('#000000'), # black
'T': parseHTMLColorStr('#ff0000'), # red
'W': parseHTMLColorStr('#804800'), # mix of A and T
'S': parseHTMLColorStr('#000080'), # mix of C and G
'M': parseHTMLColorStr('#004880'), # mix of A and C
'K': parseHTMLColorStr('#800000'), # mix of G and T
'R': parseHTMLColorStr('#004800'), # mix of A and G
'Y': parseHTMLColorStr('#800080'), # mix of C and T
'B': parseHTMLColorStr('#550055'), # mix of C, G, and T
'D': parseHTMLColorStr('#553000'), # mix of A, G, and T
'H': parseHTMLColorStr('#553055'), # mix of A, C, and T
'V': parseHTMLColorStr('#003055'), # mix of A, C, and G
'N': parseHTMLColorStr('#999') # gray
}
# Set up colors with an alpha channel to use for the lines from
# the base calls to the trace peaks.
self.pklinecolors = {}
self.pklinecolors['A'] = (self.tracecolors['A'].red,
self.tracecolors['A'].green,
self.tracecolors['A'].blue, 0.84)
self.pklinecolors['C'] = (self.tracecolors['C'].red,
self.tracecolors['C'].green,
self.tracecolors['C'].blue, 0.6)
self.pklinecolors['G'] = (self.tracecolors['G'].red,
self.tracecolors['G'].green,
self.tracecolors['G'].blue, 0.6)
self.pklinecolors['T'] = (self.tracecolors['T'].red,
self.tracecolors['T'].green,
self.tracecolors['T'].blue, 0.68)
self.bottom_margin = 2
self.bcpadding = 4
self.show_confidence = True
self.sigmax = sequencetrace.getMaxTraceVal() + (
sequencetrace.getMaxTraceVal() / 12)
self.bcfontdesc = None
self.bclayout = Pango.Layout(self.drawingarea.create_pango_context())
# Get the default font used by Gtk+ and use it as the default for the
# trace display.
self.setFontDescription(getDefaultFont())
self.drawingarea.connect('draw', self.doDraw)
self.highlighted = self.seqt.getNumBaseCalls()
def __init__(self, mod_consensseq_builder):
Gtk.DrawingArea.__init__(self)
self.cons = mod_consensseq_builder
self.numseqs = self.cons.getNumSeqs()
settings = self.cons.getSettings()
self.drawprimers = (settings.getForwardPrimer() != ''
and settings.getReversePrimer() != '')
self.cons.registerObserver('consensus_changed', self.consensusChanged)
# Initialize drawing settings.
self.basecolors = {
'A': parseHTMLColorStr('#009000'), # green
'C': parseHTMLColorStr('#0000ff'), # blue
'G': parseHTMLColorStr('#000000'), # black
'T': parseHTMLColorStr('#ff0000'), # red
'W': parseHTMLColorStr('#804800'), # mix of A and T
'S': parseHTMLColorStr('#000080'), # mix of C and G
'M': parseHTMLColorStr('#004880'), # mix of A and C
'K': parseHTMLColorStr('#800000'), # mix of G and T
'R': parseHTMLColorStr('#004800'), # mix of A and G
'Y': parseHTMLColorStr('#800080'), # mix of C and T
'B': parseHTMLColorStr('#550055'), # mix of C, G, and T
'D': parseHTMLColorStr('#553000'), # mix of A, G, and T
'H': parseHTMLColorStr('#553055'), # mix of A, C, and T
'V': parseHTMLColorStr('#003055'), # mix of A, C, and G
'N': parseHTMLColorStr('#999'), # gray
'-': parseHTMLColorStr('#000'), # black
' ': parseHTMLColorStr('#999')
}
self.bgcolors = {
# These are mostly lighter versions of the foreground colors above.
'A': parseHTMLColorStr('#cfc'),
'C': parseHTMLColorStr('#ccf'),
'G': parseHTMLColorStr('#ccc'),
'T': parseHTMLColorStr('#fcc'),
'W': parseHTMLColorStr('#DFD1BF'), # mix of A and T
'S': parseHTMLColorStr('#BFBFDF'), # mix of C and G
'M': parseHTMLColorStr('#BFD1DF'), # mix of A and C
'K': parseHTMLColorStr('#DFBFBF'), # mix of G and T
'R': parseHTMLColorStr('#BFD1BF'), # mix of A and G
'Y': parseHTMLColorStr('#DFBFDF'), # mix of C and T
'B': parseHTMLColorStr('#D5BFD5'), # mix of C, G, and T
'D': parseHTMLColorStr('#D5CBBF'), # mix of A, G, and T
'H': parseHTMLColorStr('#D5CBD5'), # mix of A, C, and T
'V': parseHTMLColorStr('#BFCBD5'), # mix of A, C, and G
'N': parseHTMLColorStr('#fff'),
'-': parseHTMLColorStr('#ff9')
}
# Calculate inverses of the main colors for drawing
# selected/highlighted bases.
self.basecolors_inv = {}
for base in self.basecolors:
self.basecolors_inv[base] = getInverseColor(self.basecolors[base])
self.bgcolors_inv = {}
for base in self.bgcolors:
self.bgcolors_inv[base] = getInverseColor(self.bgcolors[base])
# The space before the top of the alignment and after the bottom of the
# consensus sequence.
self.margins = 6
# The space between the alignment and the consensus sequence.
self.padding = 6
# The location of the top of the alignment.
self.al_top = self.margins
self.txtlayout = Pango.Layout(self.create_pango_context())
# The working width and height of the current font, in pixels.
self.fheight = -1
self.fwidth = -1
# Get the default font used by Gtk+ and use it as the default for the
# sequence display.
self.setFontDescription(getDefaultFont())
# The index of the currently highlighted position in the alignment.
self.lastx = -1
# The index of the currently selected (and highlighted) position in the
# alignment.
self.highlighted = -1
# Keep track of location of an active selection on the consensus
# sequence. The values are interpreted such that the lower value (which
# could be either start or end) is the first selected position, and the
# higher value is 1 beyond the last selected position.
self.consselect_start = -1
self.consselect_end = -1
# Indicates if the user is actively making a selection on the consensus
# sequence.
self.selecting_active = False
# Set up event handling.
self.connect('destroy', self.onDestroy)
self.connect('draw', self.onDraw)
self.set_events(Gdk.EventMask.BUTTON_PRESS_MASK
| Gdk.EventMask.BUTTON_RELEASE_MASK
| Gdk.EventMask.POINTER_MOTION_MASK
| Gdk.EventMask.POINTER_MOTION_HINT_MASK
| Gdk.EventMask.LEAVE_NOTIFY_MASK)
self.connect('button-press-event', self.mouseClick)
self.connect('button-release-event', self.mouseRelease)
self.connect('motion-notify-event', self.mouseMove)
self.connect('leave-notify-event', self.mouseLeave)
self.clickable_cursor = Gdk.Cursor.new(Gdk.CursorType.HAND2)
self.text_cursor = Gdk.Cursor.new(Gdk.CursorType.XTERM)
self.curr_cursor = None
# initialize the observable events for this class
self.defineObservableEvents([
'alignment_clicked',
'consensus_clicked',
# The 'selection_state' event is triggered when the selection state
# changes from no selection to one or more bases selected.
'selection_state'
])