def __init__(self):
"""
2008-01-30
"""
program_path = os.path.dirname(sys.argv[0])
xml = gtk.glade.XML(os.path.join(program_path, 'GenomeBrowser.glade'))
xml.signal_autoconnect(self)
self.xml = xml
self.app1 = xml.get_widget("app1")
self.app1.connect("delete_event", gtk.main_quit)
#self.app1.set_default_size(1200, 800)
self.vbox_matplotlib = xml.get_widget('vbox_matplotlib')
# matplotlib canvas
fig = Figure(figsize=(8,8))
self.canvas_matplotlib = FigureCanvas(fig) # a gtk.DrawingArea
self.canvas_matplotlib.set_size_request(600,400)
self.canvas_matplotlib.mpl_connect('pick_event', self.on_canvas_pick)
self.vbox_matplotlib.pack_start(self.canvas_matplotlib)
#matplotlib axes
#self.ax = fig.add_subplot(111)
axe_y_offset1 = 0.05 #y_offset for axe_LD, axe_strain_pca, axe_phenotype, axe_map
axe_height1 = 0.15 #height of axe_LD or axe_snp_matrix
axe_y_offset2 = axe_y_offset1+axe_height1
axe_height2 = 0.75 #height of axe_gene_model
axe_y_offset3 = axe_y_offset2+axe_height2
axe_x_offset1 = 0.1 #
axe_width1 = 0.85
axe_x_offset2 = axe_x_offset1 + axe_width1
self.ax = fig.add_axes([axe_x_offset1, axe_y_offset2, axe_width1, axe_height2], frameon=False)
self.ax.grid(True, alpha=0.3)
#self.ax.set_xticklabels([]) #remove xtick labels on ax1 because axe_LD's xtick labels cover this.
self.axe_gene_model = fig.add_axes([axe_x_offset1, axe_y_offset1, axe_width1, axe_height1], frameon=False, sharex=self.ax)
#axe_gene_model.set_xticks([]) #this will set ax1's xticks off as well because the x-axis is shared.
self.axe_gene_model.set_yticks([])
# matplotlib toolbar
self.toolbar = NavigationToolbar(self.canvas_matplotlib, self.app1)
self.vbox_matplotlib.pack_start(self.toolbar, False, False)
self.textview_output = xml.get_widget('textview_output')
self.textbuffer_output = self.textview_output.get_buffer()
#redirect stdout/stderr to textbuffer_output
t_table=self.textbuffer_output.get_tag_table()
tag_err=gtk.TextTag("error")
tag_err.set_property("foreground","red")
#tag_err.set_property("font","monospace 10")
t_table.add(tag_err)
tag_out=gtk.TextTag("output")
tag_out.set_property("foreground","blue")
#tag_out.set_property("font","monospace 10")
t_table.add(tag_out)
self.dummy_out = yh_gnome.Dummy_File(self.textbuffer_output, tag_out)
self.dummy_err = yh_gnome.Dummy_File(self.textbuffer_output, tag_err)
sys.stdout = self.dummy_out
sys.stderr = self.dummy_err
self.app1.show_all()
self.filechooserdialog1 = xml.get_widget("filechooserdialog1")
self.entry_min_value_cutoff = xml.get_widget('entry_min_value_cutoff')
self.entry_max_value_cutoff = xml.get_widget('entry_max_value_cutoff')
self.filechooserdialog1.connect("delete_event", yh_gnome.subwindow_hide)
self.dialog_db_connect = xml.get_widget("dialog_db_connect")
self.dialog_db_connect.connect("delete_event", yh_gnome.subwindow_hide)
self.entry_mysql_hostname = xml.get_widget("entry_mysql_hostname")
self.entry_mysql_dbname = xml.get_widget("entry_mysql_dbname")
self.entry_postgres_hostname = xml.get_widget("entry_postgres_hostname")
self.entry_postgres_dbname = xml.get_widget("entry_postgres_dbname")
self.entry_postgres_schema = xml.get_widget("entry_postgres_schema")
self.entry_gene_annotation_picklef = xml.get_widget("entry_gene_annotation_picklef")
self.filechooserbutton_gene_annot = xml.get_widget("filechooserbutton_gene_annot")
self.dialog_preferences = xml.get_widget("dialog_preferences")
self.dialog_preferences.connect("delete_event", yh_gnome.subwindow_hide)
self.checkbutton_debug = xml.get_widget("checkbutton_debug")
self.checkbutton_stdout = xml.get_widget("checkbutton_stdout")
self.checkbutton_stderr = xml.get_widget("checkbutton_stderr")
self.entry_gene_width = xml.get_widget("entry_gene_width")
self.checkbutton_draw_gene_symbol = xml.get_widget("checkbutton_draw_gene_symbol")
self.aboutdialog1 = xml.get_widget("aboutdialog1")
self.aboutdialog1.connect("delete_event", yh_gnome.subwindow_hide)
self.dialog_cnvqc_db = xml.get_widget("dialog_cnvqc_db")
self.filechooserdialog_cnv_gada = xml.get_widget("filechooserdialog_cnv_gada")
self.mysql_conn = self.mysql_curs = self.postgres_conn = self.postgres_curs = self.db = None
self.gene_annotation = None
self.candidate_gene_set = None
self.chr_id2size = None
self.chr_id2cumu_size = None
self.chr_gap = None
self.chr_id_ls = []
self.genome_wide_results = GenomeWideResults(gap=1.0)
self.genome_wide_results.genome_wide_result_ls = []
self.genome_wide_results.genome_wide_result_obj_id2index = {}
self.artist_obj_id2data_obj_key = {}
self.yticks = []
self.yticklabels = []
self.gene_id2artist_object_id = {}
self.chr_id2gene_id_ls = {} #chr_id here is str type (db is varchar type)
self.gene_id2model = {}
self.artist_obj_id2artist_gene_id_ls = {}
self.gene_id2vspan_obj_id = {} #for the axvspan()'s drawn on the canvas
self.gene_width = 1.0
self.draw_gene_symbol_when_clicked = 0
self.debug = 0
class GenomeBrowser(object):
def __init__(self):
"""
2008-01-30
"""
program_path = os.path.dirname(sys.argv[0])
xml = gtk.glade.XML(os.path.join(program_path, 'GenomeBrowser.glade'))
xml.signal_autoconnect(self)
self.xml = xml
self.app1 = xml.get_widget("app1")
self.app1.connect("delete_event", gtk.main_quit)
#self.app1.set_default_size(1200, 800)
self.vbox_matplotlib = xml.get_widget('vbox_matplotlib')
# matplotlib canvas
fig = Figure(figsize=(8,8))
self.canvas_matplotlib = FigureCanvas(fig) # a gtk.DrawingArea
self.canvas_matplotlib.set_size_request(600,400)
self.canvas_matplotlib.mpl_connect('pick_event', self.on_canvas_pick)
self.vbox_matplotlib.pack_start(self.canvas_matplotlib)
#matplotlib axes
#self.ax = fig.add_subplot(111)
axe_y_offset1 = 0.05 #y_offset for axe_LD, axe_strain_pca, axe_phenotype, axe_map
axe_height1 = 0.15 #height of axe_LD or axe_snp_matrix
axe_y_offset2 = axe_y_offset1+axe_height1
axe_height2 = 0.75 #height of axe_gene_model
axe_y_offset3 = axe_y_offset2+axe_height2
axe_x_offset1 = 0.1 #
axe_width1 = 0.85
axe_x_offset2 = axe_x_offset1 + axe_width1
self.ax = fig.add_axes([axe_x_offset1, axe_y_offset2, axe_width1, axe_height2], frameon=False)
self.ax.grid(True, alpha=0.3)
#self.ax.set_xticklabels([]) #remove xtick labels on ax1 because axe_LD's xtick labels cover this.
self.axe_gene_model = fig.add_axes([axe_x_offset1, axe_y_offset1, axe_width1, axe_height1], frameon=False, sharex=self.ax)
#axe_gene_model.set_xticks([]) #this will set ax1's xticks off as well because the x-axis is shared.
self.axe_gene_model.set_yticks([])
# matplotlib toolbar
self.toolbar = NavigationToolbar(self.canvas_matplotlib, self.app1)
self.vbox_matplotlib.pack_start(self.toolbar, False, False)
self.textview_output = xml.get_widget('textview_output')
self.textbuffer_output = self.textview_output.get_buffer()
#redirect stdout/stderr to textbuffer_output
t_table=self.textbuffer_output.get_tag_table()
tag_err=gtk.TextTag("error")
tag_err.set_property("foreground","red")
#tag_err.set_property("font","monospace 10")
t_table.add(tag_err)
tag_out=gtk.TextTag("output")
tag_out.set_property("foreground","blue")
#tag_out.set_property("font","monospace 10")
t_table.add(tag_out)
self.dummy_out = yh_gnome.Dummy_File(self.textbuffer_output, tag_out)
self.dummy_err = yh_gnome.Dummy_File(self.textbuffer_output, tag_err)
sys.stdout = self.dummy_out
sys.stderr = self.dummy_err
self.app1.show_all()
self.filechooserdialog1 = xml.get_widget("filechooserdialog1")
self.entry_min_value_cutoff = xml.get_widget('entry_min_value_cutoff')
self.entry_max_value_cutoff = xml.get_widget('entry_max_value_cutoff')
self.filechooserdialog1.connect("delete_event", yh_gnome.subwindow_hide)
self.dialog_db_connect = xml.get_widget("dialog_db_connect")
self.dialog_db_connect.connect("delete_event", yh_gnome.subwindow_hide)
self.entry_mysql_hostname = xml.get_widget("entry_mysql_hostname")
self.entry_mysql_dbname = xml.get_widget("entry_mysql_dbname")
self.entry_postgres_hostname = xml.get_widget("entry_postgres_hostname")
self.entry_postgres_dbname = xml.get_widget("entry_postgres_dbname")
self.entry_postgres_schema = xml.get_widget("entry_postgres_schema")
self.entry_gene_annotation_picklef = xml.get_widget("entry_gene_annotation_picklef")
self.filechooserbutton_gene_annot = xml.get_widget("filechooserbutton_gene_annot")
self.dialog_preferences = xml.get_widget("dialog_preferences")
self.dialog_preferences.connect("delete_event", yh_gnome.subwindow_hide)
self.checkbutton_debug = xml.get_widget("checkbutton_debug")
self.checkbutton_stdout = xml.get_widget("checkbutton_stdout")
self.checkbutton_stderr = xml.get_widget("checkbutton_stderr")
self.entry_gene_width = xml.get_widget("entry_gene_width")
self.checkbutton_draw_gene_symbol = xml.get_widget("checkbutton_draw_gene_symbol")
self.aboutdialog1 = xml.get_widget("aboutdialog1")
self.aboutdialog1.connect("delete_event", yh_gnome.subwindow_hide)
self.dialog_cnvqc_db = xml.get_widget("dialog_cnvqc_db")
self.filechooserdialog_cnv_gada = xml.get_widget("filechooserdialog_cnv_gada")
self.mysql_conn = self.mysql_curs = self.postgres_conn = self.postgres_curs = self.db = None
self.gene_annotation = None
self.candidate_gene_set = None
self.chr_id2size = None
self.chr_id2cumu_size = None
self.chr_gap = None
self.chr_id_ls = []
self.genome_wide_results = GenomeWideResults(gap=1.0)
self.genome_wide_results.genome_wide_result_ls = []
self.genome_wide_results.genome_wide_result_obj_id2index = {}
self.artist_obj_id2data_obj_key = {}
self.yticks = []
self.yticklabels = []
self.gene_id2artist_object_id = {}
self.chr_id2gene_id_ls = {} #chr_id here is str type (db is varchar type)
self.gene_id2model = {}
self.artist_obj_id2artist_gene_id_ls = {}
self.gene_id2vspan_obj_id = {} #for the axvspan()'s drawn on the canvas
self.gene_width = 1.0
self.draw_gene_symbol_when_clicked = 0
self.debug = 0
def load_data(self, mysql_curs, postgres_curs):
"""
2008-02-04 update the info related to chromosome , position in toolbar
2008-02-01
read the input data
chr_id2cumu_size has an extra fake chromosome (0) compared to chr_id2size
chr_id is all changed into str type
"""
from variation.src.common import get_chr_id2size, get_chr_id2cumu_size
chr_id_int2size = get_chr_id2size(mysql_curs)
self.chr_id2size = {} #change the type of chr_id into string type
for chr_id_int, size in chr_id_int2size.iteritems():
self.chr_id2size[str(chr_id_int)] = size
#chr_id2cumu_size has an extra fake chromosome (0) compared to chr_id2size
data_ls = get_chr_id2cumu_size(self.chr_id2size)
self.chr_id2cumu_size, self.chr_gap, self.chr_id_ls = data_ls[:3]
#2008-02-04 update the info related to chromosome , position in toolbar
if self.debug:
print 'self.chr_id2size', self.chr_id2size
for chr_id in self.chr_id2size:
print type(chr_id)
print 'self.chr_id2cumu_size', self.chr_id2cumu_size
for chr_id in self.chr_id2cumu_size:
print type(chr_id)
print 'self.chr_id_ls', self.chr_id_ls
for chr_id in self.chr_id_ls:
print type(chr_id)
self.toolbar.update_chr_info(self.chr_id2size, self.chr_id2cumu_size, self.chr_gap, self.chr_id_ls)
def getXposition(self, chr, pos):
chr = str(chr)
if getattr(self, 'chr_id2cumu_size', None) is None:
self.load_data(self.mysql_curs, self.postgres_curs)
this_chr_starting_pos_on_plot = self.chr_id2cumu_size[chr]-self.chr_id2size[chr]-self.chr_gap
x = this_chr_starting_pos_on_plot + pos
return x
def plot(self, ax, canvas, genome_wide_result, draw_line_as_point=True, draw_cnv_block=True):
"""
2008-05-28
input is genome_wide_result
chr_id2cumu_size, chr_id2size, chr_gap hidden from arguments
2008-02-04
chromosome is converted to str type
2008-02-01
draw the p-value, snp position, and chromosome boundary
"""
sys.stderr.write("Plotting %s ..."%genome_wide_result.name)
#ax.clear()
genome_wide_result_id = id(genome_wide_result)
x_ls = []
y_ls = []
plot_together = True
for data_obj in genome_wide_result.data_obj_ls:
y_pos = genome_wide_result.base_value - genome_wide_result.min_value + data_obj.value
x_pos = self.getXposition(data_obj.chromosome, data_obj.position)
if data_obj.stop_position is not None and draw_cnv_block==True:
x_stop_pos = self.getXposition(data_obj.chromosome, data_obj.stop_position)
xs = [x_pos, x_stop_pos, x_stop_pos, x_pos]
y_base_pos = genome_wide_result.base_value - genome_wide_result.min_value + 0
ys = [y_pos, y_pos, y_base_pos, y_base_pos]
artist_obj = Polygon(zip(xs,ys), facecolor='g', alpha=0.8, linewidth=0.5) #linewidth=0.7
ax.add_patch(artist_obj)
artist_obj_id = id(artist_obj)
plot_together = False
if data_obj.stop_position is not None and draw_line_as_point==False: #bigger than 100k, then a line
x_stop_pos = self.getXposition(data_obj.chromosome, data_obj.stop_position)
x_ls.append([(x_pos, y_pos), (x_stop_pos, y_pos)])
#artist_obj = Line2D([x_pos, y_pos], [x_stop_pos, y_pos], picker=True)
else:
if draw_line_as_point and data_obj.stop_position is not None:
x_stop_pos = self.getXposition(data_obj.chromosome, data_obj.stop_position)
x_pos = (x_pos+x_stop_pos)/2.0
x_ls.append(x_pos)
y_ls.append(y_pos)
#artist_obj = Circle((x_pos, y_pos), picker=True)
if plot_together:
if len(y_ls)>0:
artist_obj = ax.scatter(x_ls, y_ls, s=10, faceted=False, picker=True)
else:
artist_obj = LineCollection(x_ls, picker=True)
ax.add_artist(artist_obj)
artist_obj_id = id(artist_obj)
self.artist_obj_id2data_obj_key[artist_obj_id] = [genome_wide_result_id, None]
y_base_value = genome_wide_result.base_value
y_top_value = genome_wide_result.base_value + genome_wide_result.max_value - genome_wide_result.min_value
if self.debug:
print "y_base_value", y_base_value
print 'y_top_value', y_top_value
self.yticks.append(y_base_value)
self.yticks.append(y_top_value)
ax.set_yticks(self.yticks)
self.yticklabels.append('%s %.2f'%(genome_wide_result.name, genome_wide_result.min_value))
self.yticklabels.append('%s %.2f'%(genome_wide_result.name, genome_wide_result.max_value))
ax.set_yticklabels(self.yticklabels)
"""
ax.add_artist(g_artist)
artist_obj_id = id(g_artist)
self.artist_obj_id2artist_gene_id_ls[artist_obj_id] = [g_artist, gene_id]
self.gene_id2artist_object_id[gene_id] = artist_obj_id
x_ls = []
y_ls = []
max_pvalue = 0
for i in range(len(snp_pos_ls)):
chr, pos = snp_pos_ls[i]
chr = str(chr)
this_chr_starting_pos_on_plot = chr_id2cumu_size[chr]-chr_id2size[chr]-chr_gap
x = this_chr_starting_pos_on_plot + pos
x_ls.append(x)
pvalue = pvalue_ls[i]
if pvalue > max_pvalue:
max_pvalue = pvalue
y_ls.append(pvalue)
ax.plot(x_ls, y_ls, '.', picker=3) #3 points tolerance
"""
#draw the chromosome boundary
for chr_id, cumu_size in self.chr_id2cumu_size.iteritems():
ax.vlines(cumu_size, y_base_value, y_top_value, color='k')
canvas.draw()
sys.stderr.write("Done.\n")
def respond2GeneObjPicker(self, event, artist_obj_id, artist_obj_id2artist_gene_id_ls, gene_annotation,\
ax=None, draw_gene_symbol_when_clicked=False, canvas_matplotlib=None):
"""
2008-12-17
a common function specifying how to respond to picker events of
both gene models in axe_gene_model and vertical gene spans in ax
called by on_canvas_pick()
"""
gene_id = artist_obj_id2artist_gene_id_ls[artist_obj_id][1]
gene_model = gene_annotation.gene_id2model[gene_id]
if len(gene_model.gene_commentaries)==0:
gene_commentary = gene_model #fake one here
else:
gene_commentary = gene_model.gene_commentaries[0]
protein_label = getattr(gene_commentary, 'protein_label', None)
if not protein_label:
protein_label = getattr(gene_commentary, 'label', '')
protein_comment = getattr(gene_commentary, 'protein_comment', None)
if not protein_comment:
protein_comment = getattr(gene_commentary, 'comment', '')
if getattr(gene_commentary, 'protein_label', None) is not None: #true gene_commentary is available
type_of_gene = getattr(gene_model, 'type_of_gene', '')
else: #it doesn't have protein, get gene_commentary_type
type_of_gene = getattr(gene_commentary, 'gene_commentary_type', '')
print '%s (gene id=%s) type_of_gene: %s. chromosome: %s. start: %s. stop: %s. strand: %s.'%\
(gene_model.gene_symbol, gene_id, type_of_gene, gene_model.chromosome, \
gene_model.start, gene_model.stop, gene_model.strand)
print '\t protein_label: %s.'%protein_label
print '\t protein_comment: %s.'%protein_comment
if draw_gene_symbol_when_clicked:
if ax:
ax.text(event.mouseevent.xdata, event.mouseevent.ydata, gene_model.gene_symbol, size=8)
if canvas_matplotlib:
canvas_matplotlib.draw()
def on_canvas_pick(self, event):
"""
2008-11-12
display more information (maf, genotype_var_perc, comment) of data_obj (SNP) if they exist
2008-05-28
pick from collection
2008-01-31 copied from examples/pick_event_demo.py from matplotlib source code
"""
if self.debug:
print dir(event)
print event.artist
print dir(event.artist)
print type(event.artist)
"""
if isinstance(event.artist, Line2D):
thisline = event.artist
xdata = thisline.get_xdata()
ydata = thisline.get_ydata()
ind = event.ind
if self.debug:
print "indices:", ind
print 'onpick1 line:', zip(numpy.take(xdata, ind), numpy.take(ydata, ind))
for i in ind:
print "snp chromosome: %s, position: %s, pvalue: %s"%(self.snp_pos_ls[i][0], self.snp_pos_ls[i][1], self.pvalue_ls[i])
"""
if isinstance(event.artist, ExonIntronCollection): #ExonIntronCollection is also a kind of Collection
artist_obj_id = id(event.artist)
if artist_obj_id in self.artist_obj_id2artist_gene_id_ls:
self.respond2GeneObjPicker(event, artist_obj_id, self.artist_obj_id2artist_gene_id_ls, self.gene_annotation,\
ax=self.axe_gene_model, draw_gene_symbol_when_clicked=self.draw_gene_symbol_when_clicked, \
canvas_matplotlib=self.canvas_matplotlib)
else:
sys.stderr.write("%s not in artist_obj_id2artist_gene_id_ls.\n"%(artist_obj_id))
elif isinstance(event.artist, Collection) or isinstance(event.artist, LineCollection): #
artist_obj_id = id(event.artist)
if artist_obj_id in self.artist_obj_id2data_obj_key:
genome_wide_result_id, data_obj_id = self.artist_obj_id2data_obj_key[artist_obj_id]
genome_wide_result = self.genome_wide_results.get_genome_wide_result_by_obj_id(genome_wide_result_id)
for obj_index in event.ind:
if isinstance(obj_index, tuple) or isinstance(obj_index, list):
obj_index = obj_index[0]
data_obj = genome_wide_result.get_data_obj_by_obj_index(obj_index)
output_str = "genome result: %s, chromosome: %s, position: %s, "%(genome_wide_result.name, data_obj.chromosome, data_obj.position)
if data_obj.stop_position is not None:
output_str += "stop position: %s, "%(data_obj.stop_position)
output_str += '\n'
output_str += "\tscore: %s\n"%(data_obj.value)
if data_obj.maf:
output_str += "\tmaf: %s\n"%(data_obj.maf)
if data_obj.genotype_var_perc:
output_str += "\tgenotype_var_perc: %s\n"%(data_obj.genotype_var_perc)
if data_obj.comment:
output_str += "\tcomment: %s\n"%(data_obj.comment)
print output_str
else:
sys.stderr.write("%s not in artist_obj_id2data_obj_key.\n"%(artist_obj_id))
elif isinstance(event.artist, Polygon): #ExonIntronCollection is also a kind of Collection
artist_obj_id = id(event.artist)
print 'artist ID:', artist_obj_id
patch = event.artist
print 'onpick1 patch:', patch.get_verts()
if artist_obj_id in self.artist_obj_id2artist_gene_id_ls:
self.respond2GeneObjPicker(event, artist_obj_id, self.artist_obj_id2artist_gene_id_ls, self.gene_annotation,\
ax=self.ax, draw_gene_symbol_when_clicked=self.draw_gene_symbol_when_clicked, \
canvas_matplotlib=self.canvas_matplotlib)
else:
sys.stderr.write("%s not in artist_obj_id2artist_gene_id_ls.\n"%(artist_obj_id))
elif isinstance(event.artist, Rectangle):
patch = event.artist
print 'onpick1 patch:', patch.get_verts()
elif isinstance(event.artist, Text):
text = event.artist
print 'onpick1 text:', text.get_text()
def on_imagemenuitem_quit_activate(self, data=None):
"""
2008-02-01
program quits
"""
gtk.main_quit()
def on_imagemenuitem_open_activate(self, event, data=None):
self.filechooserdialog1.show_all()
def on_imagemenuitem_db_connect_activate(self, event, data=None):
self.dialog_db_connect.show_all()
def on_imagemenuitem_cnvqc_db_activate(self, event, data=None):
"""
2009-10-30
"""
self.dialog_cnvqc_db.show_all()
def on_imagemenuitem_cnv_file_activate(self, event, data=None):
"""
2009-10-30
"""
self.filechooserdialog_cnv_gada.show_all()
def on_button_filechooser_ok_clicked(self, widget, data=None):
"""
2008-12-16
allow gwr name to be specified
add function to get gwr from db based on call_method_id, analysis_method_id, phenotype_method_id
2008-10-12
add checkbutton_draw_line_as_point
add checkbutton_4th_col_stop_pos
2008-08-03
restrict the data by (chromosome, start, stop)
2008-05-31
add check button to handle log10 transformation
2008-05-28
use GenomeWideResult and etc
2008-02-14
set the window title by the input filename
"""
input_fname = self.filechooserdialog1.get_filename()
self.filechooserdialog1.hide()
if not self.mysql_conn or not self.mysql_curs:
self.db_connect()
self.app1.set_title("Genome Browser: %s"%input_fname)
checkbutton_log10_transformation = self.xml.get_widget("checkbutton_log10_transformation")
if checkbutton_log10_transformation.get_active():
do_log10_transformation = True
else:
do_log10_transformation = False
if self.entry_min_value_cutoff.get_text():
min_value_cutoff = float(self.entry_min_value_cutoff.get_text())
else:
min_value_cutoff = None
#2008-08-03
pdata = PassingData()
entry_chromosome = self.xml.get_widget("entry_chromosome")
if entry_chromosome.get_text():
pdata.chromosome = int(entry_chromosome.get_text())
entry_start = self.xml.get_widget("entry_start")
if entry_start.get_text():
pdata.start = int(entry_start.get_text())
entry_stop = self.xml.get_widget("entry_stop")
if entry_stop.get_text():
pdata.stop = int(entry_stop.get_text())
# 2009-10-27
if self.entry_max_value_cutoff.get_text():
pdata.max_value_cutoff = float(self.entry_max_value_cutoff.get_text())
else:
pdata.max_value_cutoff = None
# 2009-10-27
checkbutton_OR_min_max = self.xml.get_widget("checkbutton_OR_min_max")
if checkbutton_OR_min_max.get_active():
pdata.OR_min_max = True
else:
pdata.OR_min_max = False
checkbutton_4th_col_stop_pos = self.xml.get_widget("checkbutton_4th_col_stop_pos")
if checkbutton_4th_col_stop_pos.get_active():
pdata.is_4th_col_stop_pos = True
else:
pdata.is_4th_col_stop_pos = False
checkbutton_draw_line_as_point = self.xml.get_widget("checkbutton_draw_line_as_point")
if checkbutton_draw_line_as_point.get_active():
draw_line_as_point= True
else:
draw_line_as_point = False
entry_gwr_name = self.xml.get_widget("entry_gwr_name")
if entry_gwr_name.get_text():
pdata.gwr_name = entry_gwr_name.get_text()
else:
pdata.gwr_name = None
entry_call_method_id = self.xml.get_widget("entry_call_method_id")
call_method_id = entry_call_method_id.get_text()
entry_analysis_method_id = self.xml.get_widget("entry_analysis_method_id")
analysis_method_id = entry_analysis_method_id.get_text()
entry_phenotype_method_id = self.xml.get_widget("entry_phenotype_method_id")
phenotype_method_id = entry_phenotype_method_id.get_text()
if call_method_id and analysis_method_id and phenotype_method_id:
call_method_id = int(call_method_id)
analysis_method_id = int(analysis_method_id)
phenotype_method_id = int(phenotype_method_id)
rows = Stock_250kDB.ResultsMethod.query.filter_by(call_method_id=call_method_id).filter_by(analysis_method_id=analysis_method_id).\
filter_by(phenotype_method_id=phenotype_method_id).filter_by(results_method_type_id=1)
if rows.count()==1:
rm = rows.first()
elif rows.count()==0:
sys.stderr.write("No result fetched from db based on call_method_id=%s, analysis_method_id=%s, phenotype_method_id=%s.\n"%\
(call_method_id, analysis_method_id, phenotype_method_id))
rm = None
else:
sys.stderr.write("First result out of %s results fetched from db based on call_method_id=%s, analysis_method_id=%s, phenotype_method_id=%s.\n"%\
(rows.count(), call_method_id, analysis_method_id, phenotype_method_id))
rm = rows.first()
if rm:
input_fname = rm.filename
pdata.gwr_name = '%s_%s_%s'%(rm.analysis_method.short_name, rm.phenotype_method_id, rm.phenotype_method.short_name)
genome_wide_result = getGenomeWideResultFromFile(input_fname, min_value_cutoff, do_log10_transformation, pdata)
if len(genome_wide_result.data_obj_ls)>0:
self.genome_wide_results.add_genome_wide_result(genome_wide_result)
#self.load_data(input_fname, self.mysql_curs, self.postgres_curs)
self.plot(self.ax, self.canvas_matplotlib, self.genome_wide_results.genome_wide_result_ls[-1], draw_line_as_point=draw_line_as_point)
else:
sys.stderr.write("No data in %s under min_value_cutoff=%s. Maybe min_value_cutoff is too high.\n"%(input_fname, min_value_cutoff))
def on_button_filechooser_cancel_clicked(self, widget, data=None):
self.filechooserdialog1.hide()
def on_button_dialog_db_connect_cancel_clicked(self, widget, data=None):
self.dialog_db_connect.hide()
def on_button_dialog_db_connect_clicked(self, widget, data=None):
self.dialog_db_connect.hide()
self.db_connect()
def on_button_cnvqc_ok_clicked(self, widget, data=None):
"""
2009-10-30
"""
self.dialog_cnvqc_db.hide()
if not self.mysql_conn or not self.mysql_curs:
self.db_connect()
entry_cnv_qc_accession_id = self.xml.get_widget("entry_cnv_qc_accession_id")
cnv_qc_accession_id = entry_cnv_qc_accession_id.get_text()
if cnv_qc_accession_id:
cnv_qc_accession_id = int(cnv_qc_accession_id)
else:
sys.stderr.write("Accession id is not given.\n")
return
entry_cnv_type_id = self.xml.get_widget("entry_cnv_type_id")
cnv_type_id = entry_cnv_type_id.get_text()
if cnv_type_id:
cnv_type_id = int(cnv_type_id)
else:
cnv_type_id = None
entry_cnv_qc_min_size = self.xml.get_widget("entry_cnv_qc_min_size")
cnv_qc_min_size = entry_cnv_qc_min_size.get_text()
if cnv_qc_min_size:
cnv_qc_min_size = int(cnv_qc_min_size)
else:
cnv_qc_min_size = None
entry_cnv_qc_min_no_of_probes = self.xml.get_widget("entry_cnv_qc_min_no_of_probes")
cnv_qc_min_no_of_probes = entry_cnv_qc_min_no_of_probes.get_text()
if cnv_qc_min_no_of_probes:
cnv_qc_min_no_of_probes = int(cnv_qc_min_no_of_probes)
else:
cnv_qc_min_no_of_probes = None
genome_wide_result = self.db.getCNVQCInGWA(cnv_qc_accession_id, cnv_type_id=cnv_type_id, min_size=cnv_qc_min_size,\
min_no_of_probes=cnv_qc_min_no_of_probes)
if len(genome_wide_result.data_obj_ls)>0:
self.genome_wide_results.add_genome_wide_result(genome_wide_result)
#self.load_data(input_fname, self.mysql_curs, self.postgres_curs)
self.plot(self.ax, self.canvas_matplotlib, self.genome_wide_results.genome_wide_result_ls[-1], draw_cnv_block=True)
else:
sys.stderr.write("No CNV QC data for accession_id=%s, cnv_type=%s, min_size=%s, min_no_of_probes=%s.\n"%\
(cnv_qc_accession_id, cnv_type_id, cnv_qc_min_size, cnv_qc_min_no_of_probes))
def on_button_cnvqc_cancel_clicked(self, widget, data=None):
"""
2009-10-30
"""
self.dialog_cnvqc_db.hide()
def on_button_cnv_gada_ok_clicked(self, widget, data=None):
"""
2009-10-30
get CNVs from GADA output file
"""
input_fname = self.filechooserdialog_cnv_gada.get_filename()
self.filechooserdialog_cnv_gada.hide()
if not self.mysql_conn or not self.mysql_curs:
self.db_connect()
entry_cnv_array_id = self.xml.get_widget("entry_cnv_array_id")
array_id = entry_cnv_array_id.get_text()
if array_id:
array_id = int(array_id)
else:
sys.stderr.write("Array id is not given.\n")
return
entry_cnv_max_amp = self.xml.get_widget("entry_cnv_max_amp")
max_amp = entry_cnv_max_amp.get_text()
if max_amp:
max_amp = float(max_amp)
else:
max_amp = None
entry_cnv_min_amp = self.xml.get_widget("entry_cnv_min_amp")
min_amp = entry_cnv_min_amp.get_text()
if min_amp:
min_amp = float(min_amp)
else:
min_amp = None
entry_cnv_min_size = self.xml.get_widget("entry_cnv_min_size")
min_size = entry_cnv_min_size.get_text()
if min_size:
min_size = int(min_size)
else:
min_size = None
entry_cnv_min_no_of_probes = self.xml.get_widget("entry_cnv_min_no_of_probes")
min_no_of_probes = entry_cnv_min_no_of_probes.get_text()
if min_no_of_probes:
min_no_of_probes = int(min_no_of_probes)
else:
min_no_of_probes = None
input_fname_ls = [input_fname]
genome_wide_result = getCNVDataFromFileInGWA(input_fname_ls, array_id, max_amp=max_amp, min_amp=min_amp, min_size=min_size,\
min_no_of_probes=min_no_of_probes)
if len(genome_wide_result.data_obj_ls)>0:
self.genome_wide_results.add_genome_wide_result(genome_wide_result)
#self.load_data(input_fname, self.mysql_curs, self.postgres_curs)
self.plot(self.ax, self.canvas_matplotlib, self.genome_wide_results.genome_wide_result_ls[-1], draw_cnv_block=True)
else:
sys.stderr.write("No CNV data for array_id=%s, max_amp=%s, min_amp=%s, min_size=%s, min_no_of_probes=%s.\n"%\
(array_id, max_amp, min_amp, min_size, min_no_of_probes))
def on_button_cnv_gada_cancel_clicked(self, widget, data=None):
"""
2009-10-30
"""
self.filechooserdialog_cnv_gada.hide()
def db_connect(self):
"""
2010-1-15
pass "cls_with_db_args=self" to DrawSNPRegion.dealWithGeneAnnotation()
2009-12-09
add db_user, db_passwd to MySQLdb.connect()
2008-12-16
add gene_annotation_picklef
2008-02-01
read the data in dialog_db_connect and establish the connections to two databases
"""
sys.stderr.write("Database Connecting ...")
self.drivername = 'mysql'
self.hostname = self.entry_mysql_hostname.get_text()
self.dbname = self.entry_mysql_dbname.get_text()
self.db_user = self.xml.get_widget("entry_db_user").get_text()
self.db_passwd = self.xml.get_widget("entry_db_passwd").get_text()
import MySQLdb
try:
self.mysql_conn = MySQLdb.connect(db=self.dbname, host=self.hostname, user=self.db_user, passwd=self.db_passwd)
self.mysql_curs = self.mysql_conn.cursor()
self.db = Stock_250kDB.Stock_250kDB(drivername=self.drivername, username=self.db_user,
password=self.db_passwd, hostname=self.hostname, database=self.dbname)
self.db.setup(create_tables=False)
self.session = self.db.session
except:
sys.stderr.write('DB connection error: %s\n'%repr(sys.exc_info()))
traceback.print_exc()
if not self.gene_annotation:
gene_annotation_picklef = self.entry_gene_annotation_picklef.get_text()
self.gene_annotation = DrawSNPRegion.dealWithGeneAnnotation(gene_annotation_picklef, cls_with_db_args=self)
#2010-1-13 for postgresql. commented out
#hostname = self.entry_postgres_hostname.get_text()
#dbname = self.entry_postgres_dbname.get_text()
#schema = self.entry_postgres_schema.get_text()
#from annot.bin.codense.common import db_connect #2008-12-16 don't need postgres conn anymore
#self.postgres_conn, self.postgres_curs = db_connect(hostname, dbname, schema)
sys.stderr.write("Done.\n")
def get_gene_id2model(cls, curs, entrezgene_mapping_table='genome.entrezgene_mapping', \
annot_assembly_table = 'genome.annot_assembly', gene_table='genome.gene', \
gene2go_table='genome.gene2go', tax_id=3702):
"""
2008-09-24
turn gene_id into integer
2008-08-03
schema where tables about genes are from is renamed from 'sequence' to 'genome'
2008-02-02
get all the necessary info for genes.
watch, chromosome here is varchar type (because of chromosome X, Y etc)
"""
sys.stderr.write("Getting gene_id2model and chr_id2gene_id_ls...")
from annot.bin.codense.common import pg_1d_array2python_ls
gene_id2model = {}
chr_id2gene_id_ls = {}
curs.execute("DECLARE gene_crs CURSOR FOR select e.gene_id, a.chromosome, e.start, e.stop, e.mrna_start, e.mrna_stop, e.cds_start, e.cds_stop, e.strand, g.gene_symbol, g.description, g.type_of_gene \
from %s e, %s a, %s g where e.gene_id=g.gene_id and e.genomic_gi=a.gi and e.tax_id=%s order by chromosome, start, stop"%\
(entrezgene_mapping_table, annot_assembly_table, gene_table, tax_id))
curs.execute("fetch 5000 from gene_crs")
rows = curs.fetchall()
while rows:
for row in rows:
#gene_id is integer. chromosome is varchar.
gene_id, chromosome, start, stop, mrna_start, mrna_stop, cds_start, cds_stop, strand, symbol, description, type_of_gene = row
gene_id = int(gene_id) #2008-09-24
if cds_start and cds_stop:
if type(cds_start)!=list:
cds_start = pg_1d_array2python_ls(cds_start, int)
cds_stop = pg_1d_array2python_ls(cds_stop, int)
else:
cds_start = cds_stop = None
if mrna_start and mrna_stop:
if type(mrna_stop)!=list:
mrna_start = pg_1d_array2python_ls(mrna_start, int)
mrna_stop = pg_1d_array2python_ls(mrna_stop, int)
else:
mrna_start = mrna_stop = None
if chromosome not in chr_id2gene_id_ls:
chr_id2gene_id_ls[chromosome] = []
chr_id2gene_id_ls[chromosome].append(gene_id)
if gene_id not in gene_id2model:
gene_id2model[gene_id] = GeneModel(gene_id, chromosome, symbol, description, type_of_gene, \
start, stop, mrna_start, mrna_stop, cds_start, cds_stop, strand)
curs.execute("fetch 5000 from gene_crs")
rows = curs.fetchall()
curs.execute("close gene_crs")
sys.stderr.write("Done.\n")
return gene_id2model, chr_id2gene_id_ls
get_gene_id2model = classmethod(get_gene_id2model)
def plot_one_gene(self, ax, gene_id, gene_id2model, chr_id2cumu_size, chr_id2size, chr_gap, y_value=1, gene_width=1.0):
"""
2008-12-16
defunct. DrawSNPRegion.drawGeneModel() is used in on_button_draw_annotation_clicked()
2008-02-02
draw a single gene on the canvas,
"""
gene_model = gene_id2model.get(gene_id)
if gene_model:
c_start_ls = None
c_end_ls = None
if gene_model.cds_start!=None and gene_model.cds_stop!=None:
c_start_ls = gene_model.cds_start
c_end_ls = gene_model.cds_stop
elif gene_model.mrna_start!=None and gene_model.mrna_stop!=None:
c_start_ls = gene_model.mrna_start
c_end_ls = gene_model.mrna_stop
elif gene_model.start!=None and gene_model.stop!=None:
c_start_ls = [gene_model.start]
c_end_ls = [gene_model.stop]
if c_start_ls and c_end_ls:
chromosome = gene_model.chromosome
this_chr_starting_pos_on_plot = chr_id2cumu_size[chromosome]-chr_id2size[chromosome]-chr_gap
if gene_model.strand=="1":
g_artist = Gene(c_start_ls, c_end_ls, y=y_value, x_offset=this_chr_starting_pos_on_plot, width=gene_width, alpha=0.3, facecolor='r', picker=True)
elif gene_model.strand=="-1": #to draw opposite strand, 1st is to order c_start_ls and c_end_ls in descending order. 2nd is to swap c_start_ls and c_end_ls.
#c_start_ls.reverse() #2008-02-04 it's already in descending order in db.
#c_end_ls.reverse() #2008-02-04 it's already in descending order in db.
g_artist = Gene(c_end_ls, c_start_ls, y=y_value, x_offset=this_chr_starting_pos_on_plot, width=gene_width, alpha=0.3, facecolor='r', picker=True)
else: #no arrow
g_artist = Gene(c_start_ls, c_end_ls, y=y_value, is_arrow=False, x_offset=this_chr_starting_pos_on_plot, width=gene_width, alpha=0.3, facecolor='r', picker=True)
ax.add_artist(g_artist)
artist_obj_id = id(g_artist)
self.artist_obj_id2artist_gene_id_ls[artist_obj_id] = [g_artist, gene_id]
self.gene_id2artist_object_id[gene_id] = artist_obj_id
def on_button_draw_annotation_clicked(self, widget, data=None):
"""
2008-12-16
use DrawSNPRegion.drawGeneModel() to draw gene models
2008-02-02
"""
if not self.chr_id2size:
sys.stderr.write("No genome-wide pvalue plot has been drawn yet. Do it first!\n")
return
#if not self.gene_id2model:
# self.gene_id2model, self.chr_id2gene_id_ls = self.get_gene_id2model(self.postgres_curs, tax_id=3702)
if not self.gene_annotation:
self.db_connect()
xlim = self.axe_gene_model.get_xlim()
left_chr, left_pos = get_chr_pos_from_x_axis_pos(xlim[0], self.chr_gap, self.chr_id2cumu_size, self.chr_id_ls)
right_chr, right_pos = get_chr_pos_from_x_axis_pos(xlim[1], self.chr_gap, self.chr_id2cumu_size, self.chr_id_ls)
#fake a snps_within_this_region for drawGeneModel()
snps_within_this_region = PassingData(chr_pos_ls=[[left_chr, left_pos],[right_chr, right_pos]])
base_y_value = 1
gene_width = 0.8
gene_position_cycle = 5
return_data = DrawSNPRegion.drawGeneModel(self.axe_gene_model, snps_within_this_region, self.gene_annotation, candidate_gene_set=None,\
gene_width=gene_width, gene_position_cycle=gene_position_cycle, base_y_value=base_y_value, \
gene_box_text_gap=20, label_gene=0, rotate_xy=False,\
chr_id2cumu_size=self.chr_id2cumu_size, chr_id2size=self.chr_id2size, chr_gap=self.chr_gap,\
artist_obj_id2artist_gene_id_ls=self.artist_obj_id2artist_gene_id_ls, \
gene_id2artist_object_id=self.gene_id2artist_object_id, drawGeneOnTheBoundary=False)
#set drawGeneOnTheBoundary to False because later adding text to these genes would corrupt the running program.
self.axe_gene_model.set_ylim([base_y_value-gene_width, gene_position_cycle+gene_width*2])
"""
for gene_id in self.chr_id2gene_id_ls[left_chr]:
gene_model = self.gene_id2model[gene_id]
if gene_model.start!=None and gene_model.stop!=None and gene_model.stop>left_pos and gene_id not in self.gene_id2artist_object_id:
if left_chr==right_chr: #same chromosome
if gene_model.start>right_pos: #totally out of range, skip it
continue
y_value = len(self.gene_id2artist_object_id)%4 #cycling through the y position to avoid clogging
self.plot_one_gene(self.ax, gene_id, self.gene_id2model, self.chr_id2cumu_size, self.chr_id2size, self.chr_gap, y_value=-1-y_value, gene_width=self.gene_width)
if left_chr!=right_chr:
for gene_id in self.chr_id2gene_id_ls[right_chr]:
gene_model = self.gene_id2model[gene_id]
if gene_model.start!=None and gene_model.stop!=None and gene_model.start<right_pos and gene_id not in self.gene_id2artist_object_id:
y_value = len(self.gene_id2artist_object_id)%4 #cycling through the y position to avoid clogging
self.plot_one_gene(self.ax, gene_id, self.gene_id2model, self.chr_id2cumu_size, self.chr_id2size, self.chr_gap, y_value=-1-y_value, gene_width=self.gene_width)
"""
self.canvas_matplotlib.draw()
def on_imagemenuitem_preferences_activate(self, event, data=None):
"""
2008-02-04
"""
self.dialog_preferences.show_all()
def on_button_dialog_preferences_ok_clicked(self, widget, data=None):
"""
2008-02-04
change some preferences
"""
self.dialog_preferences.hide()
if self.checkbutton_debug.get_active():
self.debug = 1
else:
self.debug = 0
if self.checkbutton_stderr.get_active():
sys.stderr = self.dummy_err
else:
sys.stderr = sys.__stderr__
if self.checkbutton_stdout.get_active():
sys.stdout = self.dummy_out
else:
sys.stdout = sys.__stdout__
if self.checkbutton_draw_gene_symbol.get_active():
self.draw_gene_symbol_when_clicked = 1
else:
self.draw_gene_symbol_when_clicked = 0
self.gene_width = float(self.entry_gene_width.get_text())
def on_button_dialog_preferences_cancel_clicked(self, widget, data=None):
"""
2008-02-04
don't change any preferences
"""
self.dialog_preferences.hide()
def on_imagemenuitem_about_activate(self, widget):
"""
2008-02-04
"""
self.aboutdialog1.show_all()
def on_imagemenuitem_cleanup_output_activate(self, widget):
"""
2008-02-04
clean up output buffer
"""
self.textbuffer_output.set_text('')
def on_checkbutton_debug_toggled(self, widget):
"""
2008-05-28
"""
if self.checkbutton_debug.get_active():
self.debug = 1
else:
self.debug = 0
def on_checkbutton_stdout_toggled(self, widget):
"""
2008-05-28
"""
if self.checkbutton_stdout.get_active():
sys.stdout = self.dummy_out
else:
sys.stdout = sys.__stdout__
def on_checkbutton_stderr_toggled(self, widget):
"""
2008-05-28
"""
if self.checkbutton_stderr.get_active():
sys.stderr = self.dummy_err
else:
sys.stderr = sys.__stderr__
def on_checkbutton_draw_gene_symbol_toggled(self, widget):
"""
2008-05-28
"""
if self.checkbutton_draw_gene_symbol.get_active():
self.draw_gene_symbol_when_clicked = 1
else:
self.draw_gene_symbol_when_clicked = 0
def on_entry_gene_width_changed(self, widget):
"""
2008-05-28
"""
self.gene_width = float(self.entry_gene_width.get_text())
def on_filechooserbutton_gene_annot_file_set(self, widget):
"""
2008-12-16
"""
self.entry_gene_annotation_picklef.set_text(self.filechooserbutton_gene_annot.get_filename())
def on_button_draw_gene_list_bars_clicked(self, widget):
"""
2008-12-16
draw vertical spans to denote the locations of genes from a candidate list
"""
if self.db is None:
self.db_connect()
if not self.chr_id2size:
sys.stderr.write("No genome-wide pvalue plot has been drawn yet. Do it first!\n")
return
entry_gene_list_id = self.xml.get_widget("entry_gene_list_id")
list_type_id = entry_gene_list_id.get_text()
comboboxentry_bar_color = self.xml.get_widget("comboboxentry_bar_color")
bar_color = comboboxentry_bar_color.get_active_text()
if not bar_color: #default is black
bar_color = 'k'
if list_type_id:
list_type_id = int(list_type_id)
self.candidate_gene_set = GeneListRankTest.dealWithCandidateGeneList(list_type_id, return_set=True)
for gene_id in self.candidate_gene_set:
gene_model = self.gene_annotation.gene_id2model[gene_id]
if gene_id in self.gene_id2vspan_obj_id:
artist_obj_id = self.gene_id2vspan_obj_id[gene_id]
artist = self.artist_obj_id2artist_gene_id_ls[artist_obj_id][0]
if artist.get_edgecolor()!=bar_color:
artist.set_edgecolor(bar_color)
if artist.get_facecolor()!=bar_color:
artist.set_facecolor(bar_color)
#artist.remove()
else:
this_chr_starting_pos_on_plot = self.chr_id2cumu_size[gene_model.chromosome]-\
self.chr_id2size[gene_model.chromosome]-self.chr_gap
xmin = this_chr_starting_pos_on_plot + gene_model.start
xmax = this_chr_starting_pos_on_plot + gene_model.stop
artist = self.ax.axvspan(xmin, xmax, edgecolor=bar_color, facecolor=bar_color, alpha=0.3, picker=6)
artist_obj_id = id(artist)
self.artist_obj_id2artist_gene_id_ls[artist_obj_id] = [artist, gene_id]
self.gene_id2vspan_obj_id[gene_id] = artist_obj_id
self.canvas_matplotlib.draw()
def on_button_adjust_gene_axis_clicked(self, widget):
"""
2008-12-19
sometimes after zoom-in/out, axe_gene_model loses track of its y-range and the gene models in it float into ax.
this function would bring the y-range of axe_gene_model into normal range.
"""
base_y_value = 1
gene_width = 0.8
gene_position_cycle = 5
self.axe_gene_model.set_ylim([base_y_value-gene_width, gene_position_cycle+gene_width*2])
self.canvas_matplotlib.draw()