def loadExpFile(self, fullpath):
name = transit_tools.basename(fullpath)
(density, meanrd, nzmeanrd, nzmedianrd, maxrd, totalrd, skew,
kurtosis) = tnseq_tools.get_wig_stats(fullpath)
if WX_VERSION > 3:
self.list_exp.InsertItem(self.index_exp, name)
self.list_exp.SetItem(self.index_exp, 1, "%1.1f" % (totalrd))
self.list_exp.SetItem(self.index_exp, 2,
"%2.1f" % (density * 100))
self.list_exp.SetItem(self.index_exp, 3, "%1.1f" % (meanrd))
self.list_exp.SetItem(self.index_exp, 4, "%d" % (maxrd))
self.list_exp.SetItem(self.index_exp, 5, "%s" % (fullpath))
else:
self.list_exp.InsertStringItem(self.index_exp, name)
self.list_exp.SetStringItem(self.index_exp, 1,
"%1.1f" % (totalrd))
self.list_exp.SetStringItem(self.index_exp, 2,
"%2.1f" % (density * 100))
self.list_exp.SetStringItem(self.index_exp, 3,
"%1.1f" % (meanrd))
self.list_exp.SetStringItem(self.index_exp, 4, "%d" % (maxrd))
self.list_exp.SetStringItem(self.index_exp, 5,
"%s" % (fullpath))
self.list_exp.Select(self.index_exp)
self.index_exp += 1
def fromGUI(self, wxobj):
""" """
# Get Annotation file
annotationPath = wxobj.annotation
if not transit_tools.validate_annotation(annotationPath):
return None
# Get selected files
ctrldata = wxobj.ctrlSelected()
if not transit_tools.validate_control_datasets(ctrldata):
return None
# Validate transposon types
types = tnseq_tools.get_file_types(ctrldata)
if "himar1" in types:
answer = transit_tools.ShowAskWarning(
"Warning: One of the selected wig files looks like a Himar1 dataset. This method is designed to work on Tn5 wig files. Proceeding will fill in missing data with zeroes. Click OK to continue."
)
if answer == wx.ID_CANCEL:
return None
# Read the parameters from the wxPython widgets
ignoreCodon = True
minread = int(
wxobj.tn5GapsReadChoice.GetString(
wxobj.tn5GapsReadChoice.GetCurrentSelection()))
NTerminus = float(wxobj.globalNTerminusText.GetValue())
CTerminus = float(wxobj.globalCTerminusText.GetValue())
replicates = wxobj.tn5GapsRepChoice.GetString(
wxobj.tn5GapsRepChoice.GetCurrentSelection())
normalization = None
LOESS = False
# Get output path
name = transit_tools.basename(ctrldata[0])
defaultFileName = "tn5_gaps_output_m%d_r%s.dat" % (minread, replicates)
defaultDir = os.getcwd()
output_path = wxobj.SaveFile(defaultDir, defaultFileName)
if not output_path:
return None
output_file = open(output_path, "w")
return self(
ctrldata,
annotationPath,
output_file,
replicates,
normalization,
LOESS,
ignoreCodon,
minread,
NTerminus,
CTerminus,
wxobj,
)
def loadExpFile(self, fullpath):
name = transit_tools.basename(fullpath)
(density, meanrd, nzmeanrd, nzmedianrd, maxrd, totalrd, skew, kurtosis) = tnseq_tools.get_wig_stats(fullpath)
self.list_exp.InsertItem(self.index_exp, name)
self.list_exp.SetItem(self.index_exp, 1, "%1.1f" % (totalrd))
self.list_exp.SetItem(self.index_exp, 2, "%2.1f" % (density*100))
self.list_exp.SetItem(self.index_exp, 3, "%1.1f" % (meanrd))
self.list_exp.SetItem(self.index_exp, 4, "%d" % (maxrd))
self.list_exp.SetItem(self.index_exp, 5, "%s" % (fullpath))
self.list_exp.Select(self.index_exp)
self.index_exp+=1
def loadCtrlFile(self, fullpath):
name = transit_tools.basename(fullpath)
(density, meanrd, nzmeanrd, nzmedianrd, maxrd, totalrd, skew, kurtosis) = tnseq_tools.get_wig_stats(fullpath)
self.list_ctrl.InsertItem(self.index_ctrl, name)
self.list_ctrl.SetItem(self.index_ctrl, 1, "%1.1f" % (totalrd))
self.list_ctrl.SetItem(self.index_ctrl, 2, "%2.1f" % (density*100))
self.list_ctrl.SetItem(self.index_ctrl, 3, "%1.1f" % (meanrd))
self.list_ctrl.SetItem(self.index_ctrl, 4, "%d" % (maxrd))
self.list_ctrl.SetItem(self.index_ctrl, 5, "%s" % (fullpath))
self.list_ctrl.Select(self.index_ctrl)
self.index_ctrl+=1
def fromGUI(self, wxobj):
""" """
#Get Annotation file
annotationPath = wxobj.annotation
if not transit_tools.validate_annotation(annotationPath):
return None
#Get selected files
ctrldata = wxobj.ctrlSelected()
if not transit_tools.validate_control_datasets(ctrldata):
return None
#Validate transposon types
if not transit_tools.validate_transposons_used(ctrldata, transposons):
return None
#Read the parameters from the wxPython widgets
samples = int(wxobj.binomialSampleText.GetValue())
burnin = int(wxobj.binomialBurnText.GetValue())
ignoreCodon = True
NTerminus = float(wxobj.globalNTerminusText.GetValue())
CTerminus = float(wxobj.globalCTerminusText.GetValue())
replicates = "Sum"
normalization = None
LOESS = False
#Get output path
name = transit_tools.basename(ctrldata[0])
defaultFileName = "binomial_output.dat"
defaultDir = os.getcwd()
output_path = wxobj.SaveFile(defaultDir, defaultFileName)
if not output_path: return None
output_file = open(output_path, "w")
return self(ctrldata,
annotationPath,
output_file,
samples=samples,
burnin=burnin,
replicates=replicates,
normalization=normalization,
LOESS=LOESS,
ignoreCodon=ignoreCodon,
NTerminus=NTerminus,
CTerminus=CTerminus,
wxobj=wxobj)
def fromGUI(self, wxobj):
""" """
#Get Annotation file
annotationPath = wxobj.annotation
if not transit_tools.validate_annotation(annotationPath):
return None
#Get selected files
ctrldata = wxobj.ctrlSelected()
if not transit_tools.validate_control_datasets(ctrldata):
return None
#Validate transposon types
types = tnseq_tools.get_file_types(ctrldata)
if 'himar1' in types:
answer = transit_tools.ShowAskWarning("Warning: One of the selected wig files looks like a Himar1 dataset. This method is designed to work on Tn5 wig files. Proceeding will fill in missing data with zeroes. Click OK to continue.")
if answer == wx.ID_CANCEL:
return None
#Read the parameters from the wxPython widgets
ignoreCodon = True
minread = int(wxobj.tn5GapsReadChoice.GetString(wxobj.tn5GapsReadChoice.GetCurrentSelection()))
NTerminus = float(wxobj.globalNTerminusText.GetValue())
CTerminus = float(wxobj.globalCTerminusText.GetValue())
replicates= wxobj.tn5GapsRepChoice.GetString(wxobj.tn5GapsRepChoice.GetCurrentSelection())
normalization = None
LOESS = False
#Get output path
name = transit_tools.basename(ctrldata[0])
defaultFileName = "tn5_gaps_output_m%d_r%s.dat" % (minread, replicates)
defaultDir = os.getcwd()
output_path = wxobj.SaveFile(defaultDir, defaultFileName)
if not output_path: return None
output_file = open(output_path, "w")
return self(ctrldata,
annotationPath,
output_file,
replicates,
normalization,
LOESS,
ignoreCodon,
minread,
NTerminus,
CTerminus, wxobj)
def fromGUI(self, wxobj):
""" """
#Get Annotation file
annotationPath = wxobj.annotation
if not transit_tools.validate_annotation(annotationPath):
return None
#Get selected files
ctrldata = wxobj.ctrlSelected()
if not transit_tools.validate_control_datasets(ctrldata):
return None
#Validate transposon types
if not transit_tools.validate_transposons_used(ctrldata, transposons):
return None
#
minread = 1
#Read the parameters from the wxPython widgets
ignoreCodon = True
NTerminus = float(wxobj.globalNTerminusText.GetValue())
CTerminus = float(wxobj.globalCTerminusText.GetValue())
replicates = "Sum"
normalization = None
LOESS = False
#Get output path
name = transit_tools.basename(ctrldata[0])
defaultFileName = "griffin_output.dat"
defaultDir = os.getcwd()
output_path = wxobj.SaveFile(defaultDir, defaultFileName)
if not output_path: return None
output_file = open(output_path, "w")
return self(ctrldata,
annotationPath,
output_file,
minread,
replicates,
normalization,
LOESS,
ignoreCodon,
NTerminus,
CTerminus, wxobj)
def fromGUI(self, wxobj):
""" """
#Get Annotation file
annotationPath = wxobj.annotation
if not transit_tools.validate_annotation(annotationPath):
return None
#Get selected files
ctrldata = wxobj.ctrlSelected()
if not transit_tools.validate_control_datasets(ctrldata):
return None
#Validate transposon types
if not transit_tools.validate_transposons_used(ctrldata, transposons):
return None
#Read the parameters from the wxPython widgets
replicates = wxobj.hmmRepChoice.GetString(wxobj.hmmRepChoice.GetCurrentSelection())
ignoreCodon = True
NTerminus = float(wxobj.globalNTerminusText.GetValue())
CTerminus = float(wxobj.globalCTerminusText.GetValue())
normalization = wxobj.hmmNormChoice.GetString(wxobj.hmmNormChoice.GetCurrentSelection())
LOESS = False
LOESS = wxobj.hmmLoessCheck.GetValue()
#Get output path
name = transit_tools.basename(ctrldata[0])
defaultFileName = "hmm_output.dat"
defaultDir = os.getcwd()
output_path = wxobj.SaveFile(defaultDir, defaultFileName)
if not output_path: return None
output_file = open(output_path, "w")
return self(ctrldata,
annotationPath,
output_file,
replicates,
normalization,
LOESS,
ignoreCodon,
NTerminus,
CTerminus, wxobj)
def updateFiles(self):
self.index_stats = 0
try:
for j,row in enumerate(self.normdata):
name = transit_tools.basename(self.wigList[j])
(density, meanrd, nzmeanrd, nzmedianrd, maxrd, totalrd, skew, kurtosis) = tnseq_tools.get_data_stats(row)
self.statsListCtrl.InsertStringItem(self.index_stats, name)
self.statsListCtrl.SetStringItem(self.index_stats, 1, "%1.1f" % (density*100.0))
self.statsListCtrl.SetStringItem(self.index_stats, 2, "%1.1f" % (meanrd))
self.statsListCtrl.SetStringItem(self.index_stats, 3, "%1.1f" % (nzmeanrd))
self.statsListCtrl.SetStringItem(self.index_stats, 4, "%1.1f" % (nzmedianrd))
self.statsListCtrl.SetStringItem(self.index_stats, 5, "%d" % (maxrd))
self.statsListCtrl.SetStringItem(self.index_stats, 6, "%d" % (totalrd))
self.statsListCtrl.SetStringItem(self.index_stats, 7, "%1.1f" % (skew))
self.statsListCtrl.SetStringItem(self.index_stats, 8, "%1.1f" % (kurtosis))
print(self.qc_prefix, "Adding dataset (%d): %s" % (self.index_stats, name))
self.index_stats+=1
except Exception as e:
print(self.qc_prefix, "Error:", e)
exc_type, exc_obj, exc_tb = sys.exc_info()
fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]
print(exc_type, fname, exc_tb.tb_lineno)
def updateFiles(self):
self.index_stats = 0
try:
for j,row in enumerate(self.normdata):
name = transit_tools.basename(self.wigList[j])
(density, meanrd, nzmeanrd, nzmedianrd, maxrd, totalrd, skew, kurtosis) = tnseq_tools.get_data_stats(row)
self.statsListCtrl.InsertStringItem(self.index_stats, name)
self.statsListCtrl.SetStringItem(self.index_stats, 1, "%1.1f" % (density*100.0))
self.statsListCtrl.SetStringItem(self.index_stats, 2, "%1.1f" % (meanrd))
self.statsListCtrl.SetStringItem(self.index_stats, 3, "%1.1f" % (nzmeanrd))
self.statsListCtrl.SetStringItem(self.index_stats, 4, "%1.1f" % (nzmedianrd))
self.statsListCtrl.SetStringItem(self.index_stats, 5, "%d" % (maxrd))
self.statsListCtrl.SetStringItem(self.index_stats, 6, "%d" % (totalrd))
self.statsListCtrl.SetStringItem(self.index_stats, 7, "%1.1f" % (skew))
self.statsListCtrl.SetStringItem(self.index_stats, 8, "%1.1f" % (kurtosis))
print self.qc_prefix, "Adding dataset (%d): %s" % (self.index_stats, name)
self.index_stats+=1
except Exception as e:
print self.qc_prefix, "Error:", e
exc_type, exc_obj, exc_tb = sys.exc_info()
fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]
print(exc_type, fname, exc_tb.tb_lineno)
def addPlots(self):
try:
for i,reads in enumerate(self.normdata):
#Data
name = transit_tools.basename(self.wigList[i])
#reads,position = tnseq_tools.get_data([])
nzreads = reads[reads>0]
n_nz = len(nzreads)
truncnzreads = sorted(nzreads)[:int(n_nz*0.99)]
fig = plt.figure(facecolor='white', figsize=(5, 5), dpi=100)
ax = fig.add_subplot(111, frame_on=False)
#Plot 1
n, bins, patches = ax.hist(truncnzreads, density=1, facecolor='c', alpha=0.75, bins=100)
plt.xlabel('Reads')
plt.ylabel('Probability')
plt.title('Histogram of Non-Zero Reads\nDataset: %s' % name)
plt.grid(True)
buf = io.BytesIO()
fig.savefig(buf, format='png')
buf.seek(0)
hist_pil_img = Image.open(buf)
hist_wx_img = PilImageToWxImage( hist_pil_img )
hist_wx_bitmap = wx.BitmapFromImage(hist_wx_img)
#Plot 2
plt.clf()
ax = fig.add_subplot(111, frame_on=False)
((qtheoretical, qdata), (slope, intercept, r)) = scipy.stats.probplot(truncnzreads, dist="geom", sparams=(1.0/numpy.mean(truncnzreads),))
n_qdata = len(qdata)
#qtheoretical = qtheoretical[:int(n_qdata*0.99)]
#qdata = qdata[:int(n_qdata*0.99)]
ax.plot(qdata, qtheoretical, "ob")
maxval = max(numpy.max(qtheoretical), numpy.max(qdata))
ax.plot((0, maxval), (0, maxval), ls="-", c="r")
plt.xlabel("Data Quantiles")
plt.ylabel("Theoretical Quantiles")
plt.title('QQ-Plot with Theoretical Geom\nDataset: %s' % name)
plt.grid(True)
buf = io.BytesIO()
fig.savefig(buf, format='png')
buf.seek(0)
qq_pil_img = Image.open(buf)
qq_wx_img = PilImageToWxImage(qq_pil_img)
qq_wx_bitmap = wx.BitmapFromImage(qq_wx_img)
#Plot 3
plt.clf()
ax = fig.add_subplot(111, frame_on=False)
ax.plot(sorted(reads), "ob", linewidth=3)
plt.title('Rank Reads\nDataset: %s' % name)
plt.xlabel("Reads")
plt.ylabel("Rank")
plt.grid(True)
plt.xticks(rotation=45)
buf = io.BytesIO()
fig.savefig(buf, format='png')
buf.seek(0)
sorted_pil_img = Image.open(buf)
sorted_wx_img = PilImageToWxImage(sorted_pil_img)
sorted_wx_bitmap = wx.BitmapFromImage(sorted_wx_img)
self.plots_list.append([fig, hist_wx_bitmap, qq_wx_bitmap, sorted_wx_bitmap])
except Exception as e:
print(self.qc_prefix, "Error:", e)
exc_type, exc_obj, exc_tb = sys.exc_info()
fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]
print(exc_type, fname, exc_tb.tb_lineno)
def fromGUI(self, wxobj):
""" """
#Get Annotation file
annotationPath = wxobj.annotation
if not transit_tools.validate_annotation(annotationPath):
return None
#Get selected files
ctrldata = wxobj.ctrlSelected()
if not transit_tools.validate_control_datasets(ctrldata):
return None
#Validate transposon types
if not transit_tools.validate_transposons_used(ctrldata, transposons):
return None
#Read the parameters from the wxPython widgets
try:
minread = int(
wxobj.gumbelReadChoice.GetString(
wxobj.gumbelReadChoice.GetCurrentSelection()))
except:
warnings.warn(
"Warning: problem reading minimum read parameter. Assuming a value of '1'"
)
minread = 1
try:
samples = int(wxobj.gumbelSampleText.GetValue())
except:
warnings.warn(
"Warning: problem reading samples parameter. Assuming a value of '10000'"
)
samples = 10000
try:
burnin = int(wxobj.gumbelBurninText.GetValue())
except:
warnings.warn(
"Warning: problem reading burnin parameter. Assuming a value of '500'"
)
burnin = 500
try:
trim = int(wxobj.gumbelTrimText.GetValue())
except:
warnings.warn(
"Warning: problem reading trim parameter. Assuming a value of '1'"
)
trim = 1
try:
replicates = wxobj.gumbelRepChoice.GetString(
wxobj.gumbelRepChoice.GetCurrentSelection())
except:
warnings.warn(
"Warning: problem reading replicates parameter. Assuming a value of 'Mean'"
)
replicates = "Mean"
ignoreCodon = True
try:
NTerminus = float(wxobj.globalNTerminusText.GetValue())
except:
warnings.warn(
"Warning: problem reading NTerminus parameter. Assuming a value of '0.00'"
)
NTerminus = 0.0
try:
CTerminus = float(wxobj.globalCTerminusText.GetValue())
except:
warnings.warn(
"Warning: problem reading CTerminus parameter. Assuming a value of '0.00'"
)
CTerminus = 0.0
normalization = None
LOESS = False
#Get output path
name = transit_tools.basename(ctrldata[0])
defaultFileName = "gumbel_%s_s%d_b%d_t%d.dat" % (".".join(
name.split(".")[:-1]), samples, burnin, trim)
defaultDir = os.getcwd()
output_path = wxobj.SaveFile(defaultDir, defaultFileName)
if not output_path: return None
output_file = open(output_path, "w")
return self(ctrldata, annotationPath, output_file, samples, burnin,
trim, minread, replicates, normalization, LOESS,
ignoreCodon, NTerminus, CTerminus, wxobj)
def fromGUI(self, wxobj):
""" """
#Get Annotation file
annotationPath = wxobj.annotation
if not transit_tools.validate_annotation(annotationPath):
return None
#Get selected files
ctrldata = wxobj.ctrlSelected()
if not transit_tools.validate_control_datasets(ctrldata):
return None
#Validate transposon types
if not transit_tools.validate_transposons_used(ctrldata, transposons):
return None
#Read the parameters from the wxPython widgets
try:
minread = int(wxobj.gumbelReadChoice.GetString(wxobj.gumbelReadChoice.GetCurrentSelection()))
except:
warnings.warn("Warning: problem reading minimum read parameter. Assuming a value of '1'")
minread = 1
try:
samples = int(wxobj.gumbelSampleText.GetValue())
except:
warnings.warn("Warning: problem reading samples parameter. Assuming a value of '10000'")
samples = 10000
try:
burnin = int(wxobj.gumbelBurninText.GetValue())
except:
warnings.warn("Warning: problem reading burnin parameter. Assuming a value of '500'")
burnin = 500
try:
trim = int(wxobj.gumbelTrimText.GetValue())
except:
warnings.warn("Warning: problem reading trim parameter. Assuming a value of '1'")
trim = 1
try:
replicates = wxobj.gumbelRepChoice.GetString(wxobj.gumbelRepChoice.GetCurrentSelection())
except:
warnings.warn("Warning: problem reading replicates parameter. Assuming a value of 'Mean'")
replicates = "Mean"
ignoreCodon = True
try:
NTerminus = float(wxobj.globalNTerminusText.GetValue())
except:
warnings.warn("Warning: problem reading NTerminus parameter. Assuming a value of '0.00'")
NTerminus = 0.0
try:
CTerminus = float(wxobj.globalCTerminusText.GetValue())
except:
warnings.warn("Warning: problem reading CTerminus parameter. Assuming a value of '0.00'")
CTerminus = 0.0
normalization = None
LOESS = False
#Get output path
name = transit_tools.basename(ctrldata[0])
defaultFileName = "gumbel_%s_s%d_b%d_t%d.dat" % (".".join(name.split(".")[:-1]), samples, burnin, trim)
defaultDir = os.getcwd()
output_path = wxobj.SaveFile(defaultDir, defaultFileName)
if not output_path: return None
output_file = open(output_path, "w")
return self(ctrldata,
annotationPath,
output_file,
samples,
burnin,
trim,
minread,
replicates,
normalization,
LOESS,
ignoreCodon,
NTerminus,
CTerminus, wxobj)
def addPlots(self):
try:
for i,reads in enumerate(self.normdata):
#Data
name = transit_tools.basename(self.wigList[i])
#reads,position = tnseq_tools.get_data([])
nzreads = reads[reads>0]
n_nz = len(nzreads)
truncnzreads = sorted(nzreads)[:int(n_nz*0.99)]
fig = plt.figure(facecolor='white', figsize=(5, 5), dpi=100)
ax = fig.add_subplot(111, frame_on=False)
#Plot 1
n, bins, patches = ax.hist(truncnzreads, density=1, facecolor='c', alpha=0.75, bins=100)
plt.xlabel('Reads')
plt.ylabel('Probability')
plt.title('Histogram of Non-Zero Reads\nDataset: %s' % name)
plt.grid(True)
buf = io.BytesIO()
fig.savefig(buf, format='png')
buf.seek(0)
hist_pil_img = Image.open(buf)
hist_wx_img = PilImageToWxImage( hist_pil_img )
hist_wx_bitmap = wx.BitmapFromImage(hist_wx_img)
#Plot 2
plt.clf()
ax = fig.add_subplot(111, frame_on=False)
((qtheoretical, qdata), (slope, intercept, r)) = scipy.stats.probplot(truncnzreads, dist="geom", sparams=(1.0/numpy.mean(truncnzreads),))
n_qdata = len(qdata)
#qtheoretical = qtheoretical[:int(n_qdata*0.99)]
#qdata = qdata[:int(n_qdata*0.99)]
ax.plot(qdata, qtheoretical, "ob")
maxval = max(numpy.max(qtheoretical), numpy.max(qdata))
ax.plot((0, maxval), (0, maxval), ls="-", c="r")
plt.xlabel("Data Quantiles")
plt.ylabel("Theoretical Quantiles")
plt.title('QQ-Plot with Theoretical Geom\nDataset: %s' % name)
plt.grid(True)
buf = io.BytesIO()
fig.savefig(buf, format='png')
buf.seek(0)
qq_pil_img = Image.open(buf)
qq_wx_img = PilImageToWxImage(qq_pil_img)
qq_wx_bitmap = wx.BitmapFromImage(qq_wx_img)
#Plot 3
plt.clf()
ax = fig.add_subplot(111, frame_on=False)
ax.plot(sorted(reads), "ob", linewidth=3)
plt.title('Rank Reads\nDataset: %s' % name)
plt.xlabel("Reads")
plt.ylabel("Rank")
plt.grid(True)
plt.xticks(rotation=45)
buf = io.BytesIO()
fig.savefig(buf, format='png')
buf.seek(0)
sorted_pil_img = Image.open(buf)
sorted_wx_img = PilImageToWxImage(sorted_pil_img)
sorted_wx_bitmap = wx.BitmapFromImage(sorted_wx_img)
self.plots_list.append([fig, hist_wx_bitmap, qq_wx_bitmap, sorted_wx_bitmap])
except Exception as e:
print self.qc_prefix, "Error:", e
exc_type, exc_obj, exc_tb = sys.exc_info()
fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]
print(exc_type, fname, exc_tb.tb_lineno)
