def set_pipeline( self, *args ) :
print( "set_pipeline", *args )
print( self.pfamily )
if self.pipelineframe :
self.notebook.forget( self.pipelineframe )
if self.pfamily.get() == 'exomeseq' :
print( 'exomeseq' )
self.pipelineframe = ExomeSeqFrame( self.notebook,
'ExomeSeq', #self.pfamily.get(),
self.annotation, global_info=self )
elif self.pfamily.get() == 'genomeseq' :
print( 'genomeseq' )
self.pipelineframe = GenomeSeqFrame( self.notebook,
'GenomeSeq', #self.pfamily.get(),
self.annotation, global_info=self )
elif self.pfamily.get() == 'mirseq' :
print( 'mirseq' )
self.pipelineframe = MiRSeqFrame( self.notebook,
'miR-Seq', #self.pfamily.get(),
self.annotation, global_info=self )
elif self.pfamily.get() == 'ChIPseq' :
print( 'ChIPseq' )
self.pipelineframe = ChIPSeqFrame( self.notebook,
'ChIPseq',#self.pfamily.get(),
self.annotation, global_info=self )
elif self.pfamily.get() == 'rnaseq' :
print( 'rnaseq' )
self.pipelineframe = RNASeqFrame( self.notebook,
'RNAseq',#self.pfamily.get(),
self.annotation, global_info=self )
elif self.pfamily.get() == 'scrnaseq' :
print( 'scrnaseq' )
self.pipelineframe = scRNASeqFrame( self.notebook,
'scRNAseq',#self.pfamily.get(),
self.annotation, global_info=self )
else :
return
pass
self.notebook.select( self.pipelineframe )
def set_pipeline(self, *args):
print("set_pipeline", *args)
print(self.pfamily)
if self.pipelineframe:
self.notebook.forget(self.pipelineframe)
if self.pfamily.get() == 'exomeseq':
print('exomeseq')
self.pipelineframe = ExomeSeqFrame(
self.notebook,
'ExomeSeq', #self.pfamily.get(),
self.annotation,
global_info=self)
elif self.pfamily.get() == 'genomeseq':
print('genomeseq')
self.pipelineframe = GenomeSeqFrame(
self.notebook,
'GenomeSeq', #self.pfamily.get(),
self.annotation,
global_info=self)
elif self.pfamily.get() == 'mirseq':
print('mirseq')
self.pipelineframe = MiRSeqFrame(
self.notebook,
'miR-Seq', #self.pfamily.get(),
self.annotation,
global_info=self)
elif self.pfamily.get() == 'chipseq':
print('chipseq')
self.pipelineframe = ChIPSeqFrame(
self.notebook,
'ChIPseq', #self.pfamily.get(),
self.annotation,
global_info=self)
elif self.pfamily.get() == 'rnaseq':
print('rnaseq')
self.pipelineframe = RNASeqFrame(
self.notebook,
'RNAseq', #self.pfamily.get(),
self.annotation,
global_info=self)
else:
return
pass
self.notebook.select(self.pipelineframe)
class PipelinerGUI(Tk):
def __init__(self,parent=None):
Tk.__init__(self,parent)
self.parent = parent
self.initialize()
def initialize(self):
self.grid()
self.init_project_frame()
self.grid_columnconfigure(0,weight=1)
self.resizable(True,True)
#calling menubar main functioon
add_menubar(self)
self.geometry("650x760")
self.update()
def init_project_frame( self ) :
projframe = Frame(self)
######################
#The Project Entry Form
#
#Current design inherited from others
#is very bad. It should have been made as
#json or dictionary as is in this point
#then the subsequent coding will be much
#eaiser.
#BK
######################
BS=StringVar()
self.eprojectid = eprojectid= StringVar()
self.eorganism = eorganism=StringVar()
self.eanalyst = eanalyst=StringVar()
self.epoc = epoc=StringVar()
self.epi = epi=StringVar()
self.euser = euser=StringVar()
self.eflowcell = eflowcell=StringVar()
self.eplatform = eplatform=StringVar()
eplatform.set("Illumina")
self.technique = technique=StringVar()
self.pipehome = pipehome=StringVar()
pipehome.set(PIPELINER_HOME)
editframe = Frame( self )
editframe.grid( column=0, row=3, columnspan=3 )
projpanel1 = LabelFrame(editframe,text="Project Information")
#,fg=textLightColor,bg=baseColor)
projpanel1.pack( side = TOP, fill=X, padx=10, pady=5, expand=YES )
pipeline_panel = LabelFrame(editframe, text="Global Settings")
pipeline_panel.pack( side=TOP, fill=X, padx=10, pady=5, expand=YES )
l=Label( pipeline_panel, text="Genome:" )
l.grid(row=1,column=3,sticky=W,padx=0,pady=5)
l = Label( pipeline_panel, text="Pipeline Family:" )
l.grid(row=1,column=1,sticky=W,padx=0,pady=5)
annotations=['hg19','mm10','mm9','hg38','GRCh38']
self.annotation = annotation = StringVar()
annotation.set(annotations[0])
#annotation.trace('w', lambda *_ :settargets(annotation) )
om = OptionMenu(pipeline_panel, annotation, *annotations, command=self.set_pipeline)
#, command=lambda _:makejson("refsets"))
om.config() #bg = widgetBgColor,fg=widgetFgColor)
om["menu"].config() #bg = widgetBgColor,fg=widgetFgColor)
om.grid(row=1,column=4,sticky=W,padx=10,pady=10)
pfamilys = ['exomeseq', 'rnaseq', 'genomeseq', 'mirseq', 'ChIPseq', 'scrnaseq']
self.pfamily = pfamily = StringVar()
pfamily.set('Select a pipeline')
om = OptionMenu(pipeline_panel, pfamily, *pfamilys, command=self.set_pipeline)
#, command=lambda _:makejson(pfamily.get()))
om.config() #bg = widgetBgColor,fg=widgetFgColor)
om["menu"].config() #bg = widgetBgColor,fg=widgetFgColor)
om.grid(row=1,column=2,sticky=W,padx=10,pady=5)
#add_button = Button( pipeline_panel,
# text="Set a pipeline",
# command=self.add_pipeline
# )
#add_button.grid(row=1, column=5, sticky=W, padx=10, pady=5)
self.notebook = notebook = Notebook( editframe )
self.pipelineframe = None #the pipeline frame in the notebook frame!
projpanel2 = Frame(notebook) #,fg=textLightColor,bg=baseColor)
projpanel2.pack( side = LEFT, fill=BOTH, padx=10, pady=5, expand=YES )
notebook.add( projpanel2, text="Project Description" )
notebook.pack( side=LEFT, fill=BOTH, padx=10, pady=5, expand=YES )
Dscrollbar = Scrollbar(projpanel2)
Dscrollbar.grid(row=2,column=4,rowspan=40)
self.description =description= Text(projpanel2,
width=75,
height=28,
#bg=commentBgColor,
#fg=commentFgColor,
font=("nimbus mono bold","10"),
yscrollcommand = Dscrollbar.set)
description.delete("1.0", END)
description.insert(INSERT, "Enter CCBR Project Description and Notes here.")
#description.bind('<FocusOut>',lambda _:makejson("none"))
description.grid(row=2,column=3,sticky="e",padx=10,pady=5)
Dscrollbar['command']=description.yview
L=Label(projpanel1, text="Project Id", anchor="ne" )
#,bg=baseColor,fg=textLightColor)
E = Entry(projpanel1,
bd =2,
width=20,
#bg=entryBgColor,
#fg=entryFgColor,
textvariable=eprojectid
)
#L.pack(pady=5,padx=5)
#E.pack(pady=1,padx=5)
L.grid(row=0, column=0, sticky=W, padx=10, pady=5)
E.grid(row=0, column=2, sticky=W, padx=10, pady=5)
eprojectid.set("project")
#eprojectid.trace('w', makejson)
L2=Label(projpanel1,
text = "(Examples: CCBR-nnn,Labname or short project name)",
anchor="ne"
)#,bg="firebrick",fg="white")
L2.grid(row=0, column=3, padx=10, pady=5, sticky="w")
L=Label( projpanel1,
text="Email address",
anchor="ne")#,bg=baseColor,fg=textLightColor)
E = Entry( projpanel1,
bd =2,
width=20,
#bg=entryBgColor,
#fg=entryFgColor,
textvariable=euser)
L3 = Label(projpanel1,
text ="(Mandatory field: must use @nih.gov email address)",
anchor="ne")
L3.grid(row=1,column=3,padx=10,pady=5,sticky="w")
L.grid(row=1,column=0,sticky=W,padx=10,pady=5)
E.grid(row=1,column=2,sticky=W,padx=10,pady=5)
#euser.trace('w', makejson)
L=Label(projpanel1,text="Flow Cell ID",anchor="ne")
E = Entry(projpanel1, bd =2, width=20, textvariable=eflowcell )#, bg=entryBgColor)
L4=Label( projpanel1,
text="(Examples: FlowCellID, Labname, date or short project name)",
anchor="ne"
)#,bg="firebrick",fg="white")
L4.grid(row=2,column=3,padx=10,pady=5,sticky="w")
L.grid(row=2,column=0,sticky=W,padx=10,pady=5)
E.grid(row=2,column=2,sticky=W,padx=10,pady=5)
eflowcell.set("stats")
#eflowcell.trace('w', makejson)
Projscrollbar = Scrollbar(projframe)
Projscrollbar.grid(row=2,column=4,rowspan=30 )
self.jsonconf = jsonconf = Text( projframe,
width=80,
height=30,
#bg=projectBgColor,
#fg=projectFgColor,
font=("nimbus mono bold","11"),
yscrollcommand = Projscrollbar.set)
Projscrollbar['command']=jsonconf.yview
jsonconf.grid(row=3,column=0,sticky="e",padx=10,pady=5)
#jsonconf.bind('<FocusOut>',lambda _:makejson("none"))
def init_global_options( self ) :
pass
def set_pipeline( self, *args ) :
print( "set_pipeline", *args )
print( self.pfamily )
if self.pipelineframe :
self.notebook.forget( self.pipelineframe )
if self.pfamily.get() == 'exomeseq' :
print( 'exomeseq' )
self.pipelineframe = ExomeSeqFrame( self.notebook,
'ExomeSeq', #self.pfamily.get(),
self.annotation, global_info=self )
elif self.pfamily.get() == 'genomeseq' :
print( 'genomeseq' )
self.pipelineframe = GenomeSeqFrame( self.notebook,
'GenomeSeq', #self.pfamily.get(),
self.annotation, global_info=self )
elif self.pfamily.get() == 'mirseq' :
print( 'mirseq' )
self.pipelineframe = MiRSeqFrame( self.notebook,
'miR-Seq', #self.pfamily.get(),
self.annotation, global_info=self )
elif self.pfamily.get() == 'ChIPseq' :
print( 'ChIPseq' )
self.pipelineframe = ChIPSeqFrame( self.notebook,
'ChIPseq',#self.pfamily.get(),
self.annotation, global_info=self )
elif self.pfamily.get() == 'rnaseq' :
print( 'rnaseq' )
self.pipelineframe = RNASeqFrame( self.notebook,
'RNAseq',#self.pfamily.get(),
self.annotation, global_info=self )
elif self.pfamily.get() == 'scrnaseq' :
print( 'scrnaseq' )
self.pipelineframe = scRNASeqFrame( self.notebook,
'scRNAseq',#self.pfamily.get(),
self.annotation, global_info=self )
else :
return
pass
self.notebook.select( self.pipelineframe )
def progress( self ) :
#adding menu functionality
if self.pipelineframe :
self.pipelineframe.progress()
else :
showinfo( "No Pipeline Selected", "Select your analysis pipeline first!" )
def workflow( self ) :
#add menu_functionality
if self.pipelineframe :
self.pipelineframe.workflow()
else :
showinfo( "No Pipeline Selected", "Select your analysis pipeline first!" )
def set_pipeline(self, *args):
print("set_pipeline", *args)
print(self.pfamily.get())
print(self.annotation.get())
annotation = self.annotation.get()
set1 = [
'Select the genome', 'hg19', 'mm10', 'mm9', 'hg38', 'hs37d5',
'hs38d1', 'hg38_30_KSHV', 'hg38_HPV16', 'canFam3', 'Mmul_8.0.1',
'hg38_30', 'mm10_M21'
]
set2 = ['Select the genome', 'hg19', 'mm10', 'mm9', 'hg38']
set3 = ['Select the genome', 'GRCh38', 'mm10']
set4 = ['Select the genome', 'hg19', 'mm10', 'hg38']
if self.pipelineframe:
self.notebook.forget(self.pipelineframe)
if self.pfamily.get() == 'exomeseq':
print('exomeseq')
if not annotation in set4:
outtxt_short = "%s is not supported in this pipeline!" % (
annotation)
showinfo("WARNING", outtxt_short)
self.pipelineframe = ExomeSeqFrame(
self.notebook,
'ExomeSeq', #self.pfamily.get(),
self.annotation,
global_info=self)
elif self.pfamily.get() == 'genomeseq':
print('genomeseq')
if not annotation in set4:
outtxt_short = "%s is not supported in this pipeline!" % (
annotation)
showinfo("WARNING", outtxt_short)
self.pipelineframe = GenomeSeqFrame(
self.notebook,
'GenomeSeq', #self.pfamily.get(),
self.annotation,
global_info=self)
elif self.pfamily.get() == 'mirseq':
print('mirseq')
if not annotation in set2:
outtxt_short = "%s is not supported in this pipeline!" % (
annotation)
showinfo("WARNING", outtxt_short)
self.pipelineframe = MiRSeqFrame(
self.notebook,
'miR-Seq', #self.pfamily.get(),
self.annotation,
global_info=self)
elif self.pfamily.get() == 'ChIPseq':
print('ChIPseq')
if not annotation in set1:
outtxt_short = "%s is not supported in this pipeline!" % (
annotation)
showinfo("WARNING", outtxt_short)
self.pipelineframe = ChIPSeqFrame(
self.notebook,
'ChIPseq', #self.pfamily.get(),
self.annotation,
global_info=self)
elif self.pfamily.get() == 'rnaseq':
print('rnaseq')
if not annotation in set1:
outtxt_short = "%s is not supported in this pipeline!" % (
annotation)
showinfo("WARNING", outtxt_short)
self.pipelineframe = RNASeqFrame(
self.notebook,
'RNAseq', #self.pfamily.get(),
self.annotation,
global_info=self)
elif self.pfamily.get() == 'scrnaseq':
print('scrnaseq')
if not annotation in set3:
outtxt_short = "%s is not supported in this pipeline!" % (
annotation)
showinfo("WARNING", outtxt_short)
self.pipelineframe = scRNASeqFrame(
self.notebook,
'scRNAseq', #self.pfamily.get(),
self.annotation,
global_info=self)
else:
return
pass
self.notebook.select(self.pipelineframe)
