Merge pull request #196 from joshuabhk/master

mirseq_fix
CCBR · Feb 15, 2017 · dd6ebdf · dd6ebdf
2 parents 7764fa6 + c1a45d2
commit dd6ebdf
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Showing 3 changed files with 199 additions and 3 deletions.
diff --git a/gui/frame.py b/gui/frame.py
@@ -524,6 +524,7 @@ def cmd(self, smcommand):
             MkaS=os.popen(PIPELINER_HOME+"/makeasnake.py "+PL+" 2>&1 | tee -a "+self.workpath.get()+"/Reports/makeasnake.log").read()
             Out=os.popen("cd "+self.workpath.get()+" && snakemake " + smcommand +" 2>&1").read()
             show(Out,"CCBR Pipeliner: "+ pl + " "+smcommand,dryrunFgColor,dryrunBgColor,200,100)
+            #show(MkaS + "\n" + Out,"CCBR Pipeliner: "+ pl + " "+smcommand,dryrunFgColor,dryrunBgColor,200,100)
 
     def checklist( self ) :
         '''placeholder'''

diff --git a/gui/mirseq.py b/gui/mirseq.py
@@ -115,4 +115,198 @@ def loadfunc() :
 
         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=[]
+    ##        lbl=[]
+            for x in f:
+                  if len(x.split()) == 2:
+                     cont.append(x.split()[0])
+                     cont.append(x.split()[1])
+            D["rcontrasts"]=cont
+    #        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(), 
+                'organism': gi.eorganism.get(), 
+                'analyst': gi.eanalyst.get(), 
+                'poc': gi.epoc.get(), 
+                'pipeline': self.Pipeline.get(), 
+                'version':"1.0", 
+                'annotation': gi.annotation.get(), 
+                'datapath': self.datapath.get(), 
+                'targetspath': self.targetspath.get(), 
+                '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,
+             }
+        } 
+
+        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))
+
diff --git a/makeasnake.py b/makeasnake.py
@@ -1,12 +1,13 @@
 #!/usr/bin/env python
 import sys,os,re,subprocess
 import json
+from sys import stderr
 #from subprocess import call,Popen, PIPE, STDOUT
 
 #pathprj= os.path.dirname(sys.argv[1])
 pathprj= sys.argv[1]
-print(pathprj)
-print(pathprj+"/project.json")
+print(pathprj, file=stderr)
+print(pathprj+"/project.json", file=stderr)
 
 whereiam=os.popen("pwd").read().strip()