Esempio n. 1
0
class ExomeSeqFrame(PipelineFrame):
    def __init__(self, pipepanel, pipeline_name, *args, **kwargs):
        PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
        self.pairs = None

        eframe = self.eframe = LabelFrame(self, text="Options")
        #,fg=textLightColor,bg=baseColor)
        eframe.grid(row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5)

        label = Label(eframe,
                      text="Pipeline")  #,fg=textLightColor,bg=baseColor)
        label.grid(row=3, column=0, sticky=W, padx=10, pady=5)
        PipelineLabels = [
            "Initial QC", "Germline", 'Somatic Tumor-Normal',
            'Somatic Tumor-Only'
        ]
        Pipelines = [
            "initialqc", "exomeseq-germline", "exomeseq-somatic",
            "exomeseq-somatic-tumoronly"
        ]
        self.label2pipeline = {k: v for k, v in zip(PipelineLabels, Pipelines)}

        Pipeline = self.Pipeline = StringVar()
        PipelineLabel = self.PipelineLabel = StringVar()
        self.Pipeline = StringVar()

        PipelineLabel.set(PipelineLabels[0])

        om = OptionMenu(eframe,
                        PipelineLabel,
                        *PipelineLabels,
                        command=self.option_controller)
        #om.config()#bg = widgetBgColor,fg=widgetFgColor)
        #om["menu"].config()#bg = widgetBgColor,fg=widgetFgColor)
        #om.pack(side=LEFT,padx=20,pady=5)
        om.grid(row=3, column=1, sticky=W, padx=10, pady=5)

        targetsL = Label(eframe, text="Target Capture Kit")
        #,fg=textLightColor,bg=baseColor)
        targetsL.grid(row=5, column=0, sticky=W, padx=10, pady=5)
        targetsE = Entry(eframe, textvariable=self.targetspath, width=50)

        label_ref_text = "By default, the path to the Agilent SureSelect V7 targets file is filled in here"

        if self.genome == "hg19":
            self.targetspath.set(
                "/data/CCBR_Pipeliner/db/PipeDB/lib/Agilent_SSv7_allExons_hg19.bed"
            )
        elif self.genome == "hg38":
            self.targetspath.set(
                "/data/CCBR_Pipeliner/db/PipeDB/lib/Agilent_SSv7_allExons_hg38.bed"
            )
        else:
            self.targetspath.set(
                "/data/CCBR_Pipeliner/db/PipeDB/lib/SureSelect_mm10.bed")
            label_ref_text = "By default, the path to the Agilent SureSelect Mouse All Exon V1 targets file is filled in here"

        targetsE.grid(row=5, column=1, columnspan=6, sticky=W, padx=10, pady=5)
        self.targetspath.trace(
            'w', lambda a, b, c, x="targetspath": self.makejson(x))

        label = Label(eframe, text=label_ref_text)

        label.grid(row=6, column=0, columnspan=5, sticky=W, padx=10, pady=5)

    def option_controller(self, *args, **kwargs):
        PipelineFrame.option_controller(self)
        self.Pipeline.set(self.label2pipeline[self.PipelineLabel.get()])
        print(self.Pipeline.get())

        if self.Pipeline.get() == 'exomeseq-somatic':
            self.add_pairs(self.eframe)
            #self.dry_button.config( state="disabled" )
        elif self.Pipeline.get() != 'exomeseq-somatic':
            self.del_pairs(self.eframe)
            #if self.workpath.get() :
            #    self.dry_button.config( state='active' )

    def add_pairs(self, parent):
        if not self.pairs:
            self.pairs = LabelFrame(parent, text='Pairs')
            self.pairs_text = Text(
                self.pairs,
                width=50,
                height=8,
                #bg=projectBgColor,
                #fg=projectFgColor,
                font=("nimbus mono bold", "11"))

            self.pairs_save_button = Button(self.pairs,
                                            text="Save",
                                            command=self.writepair)

            self.pairs_load_button = Button(self.pairs,
                                            text="Load",
                                            command=self.readpair)

            #self.pairs_load_button.pack( side=BOTTOM, padx=5, pady=5 )
            #self.pairs_save_button.pack( side=BOTTOM, padx=5, pady=5 )

            self.pairs_load_button.grid(row=5, column=5, padx=10, pady=5)
            self.pairs_save_button.grid(row=5, column=6, padx=10, pady=5)
            self.pairs_text.grid(row=1,
                                 rowspan=3,
                                 column=1,
                                 columnspan=7,
                                 padx=5,
                                 pady=5)

        self.pairs.grid(row=7,
                        column=0,
                        columnspan=6,
                        sticky=W,
                        padx=20,
                        pady=10)

    def del_pairs(self, parent):
        if self.pairs:
            self.pairs.grid_forget()

    def writepair(self):
        self.writepaste('pairs', self.pairs_text)
        #self.dry_button.config( state='active' )

    def readpair(self):
        self.readpaste('pairs', self.pairs_text)
Esempio n. 2
0
class ExomeSeqFrame( PipelineFrame ) :
    def __init__(self, pipepanel, pipeline_name, *args, **kwargs) :
        PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
        self.pairs = None
        
        eframe = self.eframe = LabelFrame(self,text="Options") 
        #,fg=textLightColor,bg=baseColor)
        eframe.grid( row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5 )
        
        label = Label(eframe,text="Pipeline")#,fg=textLightColor,bg=baseColor)
        label.grid(row=3,column=0,sticky=W,padx=10,pady=5)
        Pipelines=["initialqc","exomeseq-somatic","exomeseq-germline"]
        Pipeline = self.Pipeline = StringVar()
        Pipeline.set(Pipelines[0])
        
        om = OptionMenu(eframe, Pipeline, *Pipelines, command=self.option_controller)
        #om.config()#bg = widgetBgColor,fg=widgetFgColor)
        #om["menu"].config()#bg = widgetBgColor,fg=widgetFgColor)
        #om.pack(side=LEFT,padx=20,pady=5)
        om.grid(row=3,column=1,sticky=W,padx=10,pady=5)

        targetsL=Label(eframe,
                       text="Target Capture Kit")
                       #,fg=textLightColor,bg=baseColor)
        targetsL.grid(row=5,column=0,sticky=W,padx=10,pady=5)
        targetsE = Entry(eframe,textvariable=self.targetspath, width=50)

        if self.genome=="hg19":
            self.targetspath.set( 
                "/data/CCBR_Pipeliner/db/PipeDB/lib/SS_v5_UTRs_hg19.bed" )
        else:
            self.targetspath.set(
                "/data/CCBR_Pipeliner/db/PipeDB/lib/SureSelect_mm10.bed")

        targetsE.grid(row=5,column=1,columnspan=6,sticky=W,padx=10,pady=5)
        self.targetspath.trace('w', lambda a,b,c,x="targetspath":self.makejson(x))
        label = Label (eframe, 
                       text = 
                       "By default, the path to the Agilent V5+UTR targets file is filled in here" ) 
        
        label.grid(row=6, column=0, columnspan=5, sticky=W, padx=10, pady=5)
        
        
            
    def option_controller( self, *args, **kwargs ) :
        PipelineFrame.option_controller( self )
        
        if self.Pipeline.get() == 'exomeseq-somatic' :
            self.add_pairs( self.eframe )
            #self.dry_button.config( state="disabled" )
        elif self.Pipeline.get() != 'exomeseq-somatic' :
            self.del_pairs( self.eframe )
            #if self.workpath.get() :
            #    self.dry_button.config( state='active' )
                
    
    def add_pairs( self, parent ) :
        if not self.pairs :
            self.pairs = LabelFrame(parent, text='Pairs')
            self.pairs_text = Text( self.pairs,
                             width=50,
                             height=8,
                             #bg=projectBgColor,
                             #fg=projectFgColor,
                             font=("nimbus mono bold","11")
                            )

            self.pairs_save_button = Button(self.pairs, 
                                            text="Save", 
                                            command = self.writepair )
            
            self.pairs_load_button = Button(self.pairs,
                                            text="Load",
                                            command = self.readpair )
            
            #self.pairs_load_button.pack( side=BOTTOM, padx=5, pady=5 )
            #self.pairs_save_button.pack( side=BOTTOM, padx=5, pady=5 )

            self.pairs_load_button.grid( row=5, column=5, padx=10, pady=5 )
            self.pairs_save_button.grid( row=5, column=6, padx=10, pady=5 )
            self.pairs_text.grid( row=1,  rowspan=3, 
                                 column=1,  columnspan=7,
                                 padx=5, pady=5 )

        self.pairs.grid(row=7,column=0, columnspan=6, sticky=W, padx=20, pady=10 )
        
    def del_pairs( self, parent ) :
        if self.pairs :
            self.pairs.grid_forget()
            
    def writepair( self ) :
        self.writepaste( 'pairs', self.pairs_text )
        #self.dry_button.config( state='active' )
    
    def readpair( self ) :
        self.readpaste( 'pairs', self.pairs_text )
Esempio n. 3
0
class GenomeSeqFrame( PipelineFrame ) :
    def __init__(self, pipepanel, pipeline_name, *args, **kwargs) :
        PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
        self.pairs = None
        
        eframe = self.eframe = LabelFrame(self,text="Options") 
        #,fg=textLightColor,bg=baseColor)
        eframe.grid( row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5 )
        
        label = Label(eframe,text="Pipeline")#,fg=textLightColor,bg=baseColor)
        label.grid(row=3,column=0,sticky=W,padx=10,pady=5)

        PipelineLabels = ['Initial QC', 
			  'Germline',
			  'Somatic Tumor-Normal',
                          'Somatic Tumor-Only']
        Pipelines=["initialqcgenomeseq",
                   "wgslow", 
		   'wgs-somatic',
                   'wgs-somatic-tumoronly']

        self.label2pipeline = { k:v for k,v in zip(PipelineLabels, Pipelines)}
        PipelineLabel = self.PipelineLabel = StringVar()
        Pipeline = self.Pipeline = StringVar()
        PipelineLabel.set(PipelineLabels[0])
        
        #om = OptionMenu(eframe, Pipeline, *Pipelines, command=self.option_controller)
        om = OptionMenu(eframe, PipelineLabel, *PipelineLabels, command=self.option_controller)
        om.config()#bg = widgetBgColor,fg=widgetFgColor)
        om["menu"].config()#bg = widgetBgColor,fg=widgetFgColor)
        #om.pack(side=LEFT,padx=20,pady=5)
        om.grid(row=3,column=1,sticky=W,padx=10,pady=5)
        
    def option_controller( self, *args, **kwargs ) :
        PipelineFrame.option_controller( self )

        self.Pipeline.set( self.label2pipeline[self.PipelineLabel.get()] )
        print( self.Pipeline.get() )

        if self.Pipeline.get() == 'wgs-somatic' :
            self.add_pairs( self.eframe )
            #self.dry_button.config( state="disabled" )
        elif self.Pipeline.get() != 'wgs-somatic' :
            self.del_pairs( self.eframe )
            #if self.workpath.get() :
            #    self.dry_button.config( state='active' )

    
    def add_pairs( self, parent ) :
        if not self.pairs :
            self.pairs = LabelFrame(parent, text='Pairs')
            self.pairs_text = Text( self.pairs,
                             width=50,
                             height=8,
                             #bg=projectBgColor,
                             #fg=projectFgColor,
                             font=("nimbus mono bold","11")
                            )

            self.pairs_save_button = Button(self.pairs, 
                                            text="Save", 
                                            command = self.writepair )
            
            self.pairs_load_button = Button(self.pairs,
                                            text="Load",
                                            command = self.readpair )
            
            #self.pairs_load_button.pack( side=BOTTOM, padx=5, pady=5 )
            #self.pairs_save_button.pack( side=BOTTOM, padx=5, pady=5 )

            self.pairs_load_button.grid( row=5, column=5, padx=10, pady=5 )
            self.pairs_save_button.grid( row=5, column=6, padx=10, pady=5 )
            self.pairs_text.grid( row=1,  rowspan=3, 
                                 column=1,  columnspan=7,
                                 padx=5, pady=5 )

        self.pairs.grid(row=7,column=0, columnspan=6, sticky=W, padx=20, pady=10 )
        
    def del_pairs( self, parent ) :
        if self.pairs :
            self.pairs.grid_forget()
            
    def writepair( self ) :
        self.writepaste( 'pairs', self.pairs_text )
        #self.dry_button.config( state='active' )
    
    def readpair( self ) :
        self.readpaste( 'pairs', self.pairs_text )
Esempio n. 4
0
class RNASeqFrame(PipelineFrame):
    def __init__(self, pipepanel, pipeline_name, *args, **kwargs):
        PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
        self.info = None

        eframe = self.eframe = LabelFrame(self, text="Options")
        #,fg=textLightColor,bg=baseColor)
        eframe.grid(row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5)

        label = Label(eframe,
                      text="Pipeline")  #,fg=textLightColor,bg=baseColor)
        label.grid(row=3, column=0, sticky=W, padx=10, pady=5)
        PipelineLabels = [
            "Quality Control Analysis", "Differential Expression Analysis",
            "Fusion Detection", "Variant Calling"
        ]
        Pipelines = [
            "initialqcrnaseq", "rnaseq", "rnaseqfusion", "rnaseqvargerm"
        ]

        self.label2pipeline = {k: v for k, v in zip(PipelineLabels, Pipelines)}

        PipelineLabel = self.PipelineLabel = StringVar()
        self.Pipeline = StringVar()

        PipelineLabel.set(PipelineLabels[0])
        om = OptionMenu(eframe,
                        PipelineLabel,
                        *PipelineLabels,
                        command=self.option_controller)
        om.config()  #bg = widgetBgColor,fg=widgetFgColor)
        om["menu"].config()  #bg = widgetBgColor,fg=widgetFgColor)
        #om.pack(side=LEFT,padx=20,pady=5)
        om.grid(row=3, column=1, sticky=W, padx=10, pady=5)

        rReadlens = [
            'Read Length is 50', 'Read Length is 75', 'Read Length is 100',
            'Read Length is 125', 'Read Length is 150', 'Read Length is 250'
        ]
        self.rReadlen = rReadlen = StringVar()
        rReadlen.set(rReadlens[2])
        self.om2 = OptionMenu(eframe,
                              rReadlen,
                              *rReadlens,
                              command=self.option_controller)
        #self.om2.grid(row=4,column=1,sticky=W,padx=10,pady=5)

        rStrands = [
            '0, Reads are Unstranded', '1, Reads are from Sense Strand',
            '2, Reads are from Anti-Sense Strand'
        ]
        self.rStrand = rStrand = StringVar()
        rStrand.set(rStrands[0])
        self.om3 = OptionMenu(eframe,
                              rStrand,
                              *rStrands,
                              command=self.option_controller)
        #self.om3.grid(row=5,column=1,sticky=W,padx=10,pady=5)

        rDegs = [
            "yes, Report Differentially Expressed Genes",
            "no, Do not Report Differentially Expressed Genes"
        ]
        self.rDeg = rDeg = StringVar()
        rDeg.set(rDegs[0])
        self.om4 = OptionMenu(eframe,
                              rDeg,
                              *rDegs,
                              command=self.option_controller)
        self.om4.grid(row=6, column=1, sticky=W, padx=10, pady=5)

        # Show Groups Only (For initialqcrnaseq)
        self.om_groups = LabelFrame(eframe, text="Sample Information")
        self.groups_button = Button(self.om_groups,
                                    text="Set Groups",
                                    command=self.popup_groups)
        self.groups_button.grid(row=5, column=5, padx=10, pady=5)

        #####################
        #Sample Threshold
        #####################
        self.sampleLF = sampleLF = LabelFrame(
            eframe, text="Low Abundance Gene Thresholds")

        self.rMincount = rMincount = StringVar()
        rMincount.set("0.5")
        self.rMinsamples = rMinsamples = StringVar()
        rMinsamples.set("2")

        #rMincount.trace('w', lambda a,b,c,x="rmincount": makejson(x))

        #Filter out genes < [5] read counts in < [2] samples
        #         rminsamplesL = Label(sampleLF, text="Include genes with >=") # in")
        #         rmincountE = Entry(sampleLF, bd =2, width=3, textvariable=rMincount)
        #         rmincountL = Label(sampleLF, text="CPM in  >=")
        #         rminsamplesE = Entry(sampleLF, bd =2, width=3, textvariable=rMinsamples)
        #         rminsamplesR = Label(sampleLF, text="samples")
        #
        #         rminsamplesL.grid(row=9,column=1,sticky=W,padx=10,pady=5)
        #         rmincountE.grid(row=9,column=2,sticky=W,padx=0,pady=5)
        #         rmincountL.grid(row=9,column=3,sticky=W,padx=5,pady=5)
        #         rminsamplesE.grid(row=9,column=4,sticky=W,padx=0,pady=5)
        #         rminsamplesR.grid(row=9,column=5,sticky=W,padx=10,pady=5)
        #         #rMinsamples.trace('w', lambda a,b,c,x="rmincount": makejson(x))

        sampleLF.grid(row=6,
                      column=0,
                      columnspan=4,
                      sticky=W,
                      padx=20,
                      pady=10)
        #####################

        self.add_info(eframe)
        self.option_controller()

    def option_controller(self, *args, **kwargs):

        PipelineFrame.option_controller(self)

        self.Pipeline.set(self.label2pipeline[self.PipelineLabel.get()])
        print(self.Pipeline.get())

        if self.Pipeline.get() == 'initialqcrnaseq':
            self.om4.grid_forget()
            self.sampleLF.grid_forget()
            self.info.grid_forget()
            self.om_groups.grid(row=10,
                                column=0,
                                columnspan=6,
                                sticky=W,
                                padx=20,
                                pady=10)
        elif self.Pipeline.get() == 'rnaseq':
            self.om4.grid(row=6, column=1, sticky=W, padx=10, pady=5)
            self.sampleLF.grid(row=8,
                               column=0,
                               columnspan=4,
                               sticky=W,
                               padx=20,
                               pady=10)
            self.info.grid(row=10,
                           column=0,
                           columnspan=6,
                           sticky=W,
                           padx=20,
                           pady=10)
            self.om_groups.grid_forget()
        else:
            self.om4.grid_forget()
            self.sampleLF.grid_forget()
            self.info.grid_forget()
            self.om_groups.grid_forget()

    def makejson_wrapper(self, *args, **kwargs):
        self.makejson(*args, **kwargs)

    def add_info(self, parent):
        if not self.info:
            self.info = LabelFrame(parent, text="Sample Information")
            self.groups_button = Button(self.info,
                                        text="Set Groups",
                                        command=self.popup_groups)
            self.contrasts_button = Button(self.info,
                                           text="Set Contrasts",
                                           command=self.popup_contrasts)
            self.groups_button.grid(row=5, column=5, padx=10, pady=5)
            self.contrasts_button.grid(row=5, column=6, padx=10, pady=5)

    def popup_groups(self):
        self.popup_window("Groups Information", "groups.tab")

    def popup_contrasts(self):
        self.popup_window("Contrasts Information", "contrasts.tab")

    def popup_window(self, text, filename):
        top = Toplevel()

        info = LabelFrame(top, text=text)  #"Group Information")
        info_text = Text(
            info,
            width=50,
            height=8,
            #bg=projectBgColor,
            #fg=projectFgColor,
            font=("nimbus mono bold", "11"))

        def savefunc():
            self.writepaste(filename, info_text)

        def loadfunc():
            self.readpaste(filename, info_text)

        info_save_button = Button(info, text="Save", command=savefunc)
        info_load_button = Button(info, text="Load", command=loadfunc)

        #self.pairs_load_button.pack( side=BOTTOM, padx=5, pady=5 )
        #self.pairs_save_button.pack( side=BOTTOM, padx=5, pady=5 )

        info_load_button.grid(row=5, column=5, padx=10, pady=5)
        info_save_button.grid(row=5, column=6, padx=10, pady=5)
        info_text.grid(row=1,
                       rowspan=3,
                       column=1,
                       columnspan=7,
                       padx=5,
                       pady=5)

        info.grid(row=7, column=0, columnspan=6, sticky=W, padx=20, pady=10)
        top.focus_force()

    def makejson(self, *args):
        #print(args[0])
        caller = args[0]
        #global PD
        #global UnitsBak
        #global RGbak
        D = dict()
        try:
            F = open(self.workpath.get() + "/samples", "r")
            f = F.read().split("\n")
            F.close()
            for line in f:
                L = line.split()
                a = L.pop(0)
                D[a] = L
                samples = D
        except:
            samples = {"na": "na"}

        D = dict()
        try:
            F = open(self.workpath.get() + "/pairs", "r")
            f = F.read().split()
            F.close()
            for i in range(0, len(f), 2):
                #            a=f[i].split(".")[0]
                #            b=f[i+1].split(".")[0]
                a = f[i]
                b = f[i + 1]

                D[a + "+" + b] = [a, b]

            pairs = D
        except:
            pairs = {"na": "na"}

        D = dict()
        try:
            F = open(self.workpath.get() + "/contrasts.tab", "r")
            #        f=F.read().split('\n')
            #        F.close()
            #        D["rsamps"]=f[0].split()
            #        D["rgroups"]=f[1].split()
            #        D["rcontrasts"]=f[2].split()
            #        D["rlabels"]=f[3].split()
            f = F.readlines()
            F.close()
            ##        sampl=[]
            ##        grp=[]
            cont = []
            cont_cpm_cutoff = []
            cont_mincount = []
            ##        lbl=[]
            ## contrasts.tab can have 2,3 or 4 columns
            # col 1 and 2 are group1 and group2 respectively
            # col 3 is CPM cutoff value ... if not provided 0.5 will be used
            # col 4 is either min number of sample per group that need to satisfy the cpm cutoff criteria or fraction of samples that need
            #       to satisfy the criteria... can be integer >=1 ... or fraction >=0.5 and <1
            for x in f:
                xsplit = x.split()
                if len(xsplit) == 4:
                    cont.append(xsplit[0])
                    cont.append(xsplit[1])
                    cont_cpm_cutoff.append(xsplit[2])
                    cont_mincount.append(xsplit[3])
                elif len(xsplit) == 3:
                    cont.append(xsplit[0])
                    cont.append(xsplit[1])
                    cont_cpm_cutoff.append(xsplit[2])
                    cont_mincount.append("0.5")
                elif len(xsplit) == 2:
                    cont.append(xsplit[0])
                    cont.append(xsplit[1])
                    cont_cpm_cutoff.append("0.5")
                    cont_mincount.append("0.5")

            D["rcontrasts"] = cont
            D["rcontrasts_cpm_cutoff"] = cont_cpm_cutoff
            D["rcontrasts_min_counts"] = cont_mincount
            #        contrasts["rcontrasts"]=cont
            contrasts = D
        except:
            contrasts = {"rcontrasts": "na"}
    ##        contrasts={"rsamps":"na","rgroups":"na","rcontrasts":"na","rlabels":"na"}
    ##------
        D = dict()
        try:
            F = open(self.workpath.get() + "/groups.tab", "r")
            f = F.readlines()
            F.close()
            sampl = []
            grp = []
            #        cont=[]
            lbl = []
            for x in f:
                #           if len(x.split()) == 4 or len(x.split()) == 3:
                if len(x.split()) == 3:
                    sampl.append(x.split()[0])
                    grp.append(x.split()[1])
                    lbl.append(x.split()[2])
            D["rsamps"] = sampl
            D["rgroups"] = grp
            D["rlabels"] = lbl
            #        D["rcontrasts"]="na"
            #        contrasts=D
            groups = D
        except:
            #        contrasts={"rsamps":"na","rgroups":"na","rcontrasts":"na","rlabels":"na"}
            groups = {"rsamps": "na", "rgroups": "na", "rlabels": "na"}

    ##------
        D = dict()
        FT = filetype  #.get()
        #    p = Popen("ls "+workpath.get()+"/*."+FT, shell=True, stdin=PIPE, stdout=PIPE, stderr=DEVNULL, close_fds=True)
        p = Popen("find " + self.workpath.get() +
                  " -maxdepth 1 -type l -printf '%f\n' ",
                  shell=True,
                  stdin=PIPE,
                  stdout=PIPE,
                  stderr=DEVNULL,
                  close_fds=True)
        a = p.stdout.read().decode(encoding='UTF-8').split("\n")

        RG = dict()
        b = a.pop()
        #    tkinter.messagebox.showerror("",a)
        #    if freezeunits.get()=="no":
        for i in a:

            key = re.sub(".realign", "", i.split("/")[-1])
            key = re.sub(".bai", "", key)
            key = re.sub(".bam", "", key)
            key = re.sub(".sam", "", key)
            key = re.sub(".recal", "", key)
            key = re.sub(".dedup", "", key)
            key = re.sub(".sorted", "", key)
            key = re.sub(".fin", "", key)
            key = re.sub("\.R[12]", "", key)
            key = re.sub("_R[12]", "", key)
            key = re.sub(".fastq", "", key)
            key = re.sub(".gz", "", key)
            #        key=re.sub("[\._](R[12]\.)*"+FT+"$","",i.split("/")[-1])
            #        key=re.sub(".R[12]."+FT+"$","",i.split("/")[-1])
            #        key=re.sub("([._]R[12][._])*([fin|sorted|dedup|recal|realign])*\.{0}$".format(FT),"",i.split("/")[-1])
            D[key] = key
            RG[key] = {
                'rgsm': key,
                'rglb': 'na',
                'rgpu': 'na',
                'rgpl': 'ILLUMINA',
                'rgcn': 'na'
            }
        units = D
        UnitsBak = D

        try:
            F = open(self.workpath.get() + "/rg.tab", "r")
            f = F.read().splitlines()
            F.close()
            for theLine in f:
                if not re.match("^ID", theLine):
                    (rgid, rgsm, rglb, rgpl, rgpu, rgcn) = theLine.split("\t")
                    RG[rgid] = {
                        'rgsm': rgsm,
                        'rglb': rglb,
                        'rgpu': rgpu,
                        'rgpl': rgpl,
                        'rgcn': rgcn
                    }
        except:
            pass

        RGbak = RG
        #     else:
        #         units=UnitsBak
        #         RG=RGbak
        #
        PD = dict()

        smparams = []

        for i in range(len(self.parameters)):

            if cp[i].var.get() == "1":
                smparams.append(parameters[i])

        AD = eval(
            open(join(PIPELINER_HOME,
                      self.annotation.get() + ".json"), "r").read())

        SD = AD['references']['rnaseq']['STARDIR']
        #    tkinter.messagebox.showinfo("initLock","SD={0}".format(SD))
        gi = self.global_info
        PD = {
            'project': {
                'pfamily':
                gi.pfamily.get(),
                'units':
                units,
                'samples':
                samples,
                'pairs':
                pairs,
                'id':
                gi.eprojectid.get(),
                'pi':
                gi.epi.get(),
                'pipehome':
                gi.pipehome.get(),
                'organism':
                gi.eorganism.get(),
                'analyst':
                gi.eanalyst.get(),
                'poc':
                gi.epoc.get(),
                'pipeline':
                self.Pipeline.get(),
                'version':
                "4.0",
                'annotation':
                gi.annotation.get(),
                'datapath':
                self.datapath.get(),
                'targetspath':
                self.targetspath.get(),
                'nends':
                self.nends,
                'filetype':
                filetype,
                'binset':
                "standard-bin",
                'username':
                gi.euser.get(),
                'flowcellid':
                gi.eflowcell.get(),
                'platform':
                gi.eplatform.get(),
                'custom':
                customRules,
                'efiletype':
                efiletype,
                'workpath':
                self.workpath.get(),
                'batchsize':
                batchsize,
                "smparams":
                smparams,
                "rgid":
                RG,
                "cluster":
                "cluster_medium.json",
                "description":
                gi.description.get('1.0', END),
                "technique":
                gi.technique.get(),
                "TRIM":
                "yes",
                "groups":
                groups,
                "contrasts":
                contrasts,
                "SJDBOVERHANG":
                self.rReadlen.get().split(" ")[3],
                "STRANDED":
                self.rStrand.get().split(",")[0],
                "DEG":
                self.rDeg.get().split(",")[0].lower(),
                "STARSTRANDCOL":
                "{0}".format(int(self.rStrand.get().split(",")[0]) + 2),
                "MINSAMPLES":
                self.rMinsamples.get(),
                "MINCOUNTGENES":
                self.rMincount.get(),
                "MINCOUNTJUNCTIONS":
                self.rMincount.get(),
                "MINCOUNTGENEJUNCTIONS":
                self.rMincount.get(),
                "STARDIR":
                SD + self.rReadlen.get().split(" ")[3],
                "PICARDSTRAND": [
                    "NONE", "FIRST_READ_TRANSCRIPTION_STRAND",
                    "SECOND_READ_TRANSCRIPTION_STRAND"
                ][int(self.rStrand.get().split(",")[0])]
            }
        }

        J = json.dumps(PD, sort_keys=True, indent=4, ensure_ascii=True)
        gi.jsonconf.delete("1.0", END)
        gi.jsonconf.insert(INSERT, J)
        self.saveproject(gi.jsonconf.get("1.0", END))
Esempio n. 5
0
class GenomeSeqFrame(PipelineFrame):
    def __init__(self, pipepanel, pipeline_name, *args, **kwargs):
        PipelineFrame.__init__(self, pipepanel, pipeline_name, *args, **kwargs)
        self.pairs = None

        eframe = self.eframe = LabelFrame(self, text="Options")
        #,fg=textLightColor,bg=baseColor)
        eframe.grid(row=5, column=1, sticky=W, columnspan=7, padx=10, pady=5)

        label = Label(eframe,
                      text="Pipeline")  #,fg=textLightColor,bg=baseColor)
        label.grid(row=3, column=0, sticky=W, padx=10, pady=5)

        PipelineLabels = [
            'Initial QC', 'Germline', 'Somatic Tumor-Normal',
            'Somatic Tumor-Only'
        ]
        Pipelines = [
            "initialqcgenomeseq", "wgslow", 'wgs-somatic',
            'wgs-somatic-tumoronly'
        ]

        self.label2pipeline = {k: v for k, v in zip(PipelineLabels, Pipelines)}
        PipelineLabel = self.PipelineLabel = StringVar()
        Pipeline = self.Pipeline = StringVar()
        PipelineLabel.set(PipelineLabels[0])

        #om = OptionMenu(eframe, Pipeline, *Pipelines, command=self.option_controller)
        om = OptionMenu(eframe,
                        PipelineLabel,
                        *PipelineLabels,
                        command=self.option_controller)
        om.config()  #bg = widgetBgColor,fg=widgetFgColor)
        om["menu"].config()  #bg = widgetBgColor,fg=widgetFgColor)
        #om.pack(side=LEFT,padx=20,pady=5)
        om.grid(row=3, column=1, sticky=W, padx=10, pady=5)

    def option_controller(self, *args, **kwargs):
        PipelineFrame.option_controller(self)

        self.Pipeline.set(self.label2pipeline[self.PipelineLabel.get()])
        print(self.Pipeline.get())

        if self.Pipeline.get() == 'wgs-somatic':
            self.add_pairs(self.eframe)
            #self.dry_button.config( state="disabled" )
        elif self.Pipeline.get() != 'wgs-somatic':
            self.del_pairs(self.eframe)
            #if self.workpath.get() :
            #    self.dry_button.config( state='active' )

    def add_pairs(self, parent):
        if not self.pairs:
            self.pairs = LabelFrame(parent, text='Pairs')
            self.pairs_text = Text(
                self.pairs,
                width=50,
                height=8,
                #bg=projectBgColor,
                #fg=projectFgColor,
                font=("nimbus mono bold", "11"))

            self.pairs_save_button = Button(self.pairs,
                                            text="Save",
                                            command=self.writepair)

            self.pairs_load_button = Button(self.pairs,
                                            text="Load",
                                            command=self.readpair)

            #self.pairs_load_button.pack( side=BOTTOM, padx=5, pady=5 )
            #self.pairs_save_button.pack( side=BOTTOM, padx=5, pady=5 )

            self.pairs_load_button.grid(row=5, column=5, padx=10, pady=5)
            self.pairs_save_button.grid(row=5, column=6, padx=10, pady=5)
            self.pairs_text.grid(row=1,
                                 rowspan=3,
                                 column=1,
                                 columnspan=7,
                                 padx=5,
                                 pady=5)

        self.pairs.grid(row=7,
                        column=0,
                        columnspan=6,
                        sticky=W,
                        padx=20,
                        pady=10)

    def del_pairs(self, parent):
        if self.pairs:
            self.pairs.grid_forget()

    def writepair(self):
        self.writepaste('pairs', self.pairs_text)
        #self.dry_button.config( state='active' )

    def readpair(self):
        self.readpaste('pairs', self.pairs_text)