add sample info to initialrnaseqqc gui; added mincount column to grou…

…ps.tab

Results-template/Scripts/filtersamples.py

@@ -4,17 +4,18 @@
 rscript=sys.argv[3]
 sampletable=sys.argv[4]
 rawcountsfile=sys.argv[5]
-minsamples=sys.argv[6]
-newsampletable=sys.argv[7]
-filteredcountstable=sys.argv[8]
+newsampletable=sys.argv[6]
+filteredcountstable=sys.argv[7]
 
 degdir=folderpath.strip().split("/")[-1]
 
 v1=degdir.split("DEG_")[1]
-cpm_cutoff=v1.split("_")[-1]
+minsamples=v1.split("_")[-1]
+cpm_cutoff=v1.split("_")[-2]
 
 v2=v1.split("_")
 v2.pop(-1)
+v2.pop(-1)
 v3="_".join(v2)
 g1=v3.split("-")[0]
 g2=v3.split("-")[1]

Rules/rnaseq.snakefile

@@ -23,7 +23,8 @@ def createConstrasts(cList):
     contrastsList.append("-".join(cList[i:i+2]))
   return contrastsList
 
-
+def get_cpm_cutoff(degdir,contrasts_w_cpm_cutoff_list,cpm_cutoff_list):
+	return cpm_cutoff_list[contrasts_w_cpm_cutoff_list.index(degdir)]
 
 configfile: "run.json"
 
@@ -33,10 +34,11 @@ workpath=config['project']['workpath']
 
 contrastsList = createConstrasts(config['project']['contrasts']['rcontrasts'])
 cpm_cutoff_list = config['project']['contrasts']['rcontrasts_cpm_cutoff']
+mincounts = config['project']['contrasts']['rcontrasts_min_counts']
 
 contrasts_w_cpm_cutoff_list = []
-for i in zip(contrastsList,cpm_cutoff_list):
-	contrasts_w_cpm_cutoff_list.append(str(i[0])+"_"+str(i[1]))
+for i in zip(contrastsList,cpm_cutoff_list,mincounts):
+	contrasts_w_cpm_cutoff_list.append(str(i[0])+"_"+str(i[1]))+"_"+str(i[2]))
 
 se=""
 pe=""
@@ -238,14 +240,13 @@ rule init_deg:
 		filteredcountstabs=expand(join(workpath,"DEG_{deg_dir}","RawCountFile_RSEM_genes_filtered.txt"),deg_dir=contrasts_w_cpm_cutoff_list),
 	params:
 		rname="pl:init_deg_dir",
-		scripts_dir=join(workpath,"Scripts"),
 		rscript=join(workpath,"Scripts","filtersamples.R"),
-		minsamples=config['project']['MINSAMPLES'],
 		rver=config['bin'][pfamily]['tool_versions']['RVER'],
+		pyscript=join(workpath,"Scripts","filtersamples.R"),
 	shell:"""
 for f in {output.folders};do
 if [ ! -d $f ]; then mkdir $f ;fi
-python {params.scripts_dir}/filtersamples.py $f {params.rver} {params.rscript} {input.samtab} {input.rawcountstab} {params.minsamples} $f/sampletable.txt $f/RawCountFile_RSEM_genes_filtered.txt
+python {params.pyscript} $f {params.rver} {params.rscript} {input.samtab} {input.rawcountstab} $f/sampletable.txt $f/RawCountFile_RSEM_genes_filtered.txt
 done
 """
 

gui/rnaseq.py

@@ -126,7 +126,7 @@ def option_controller( self, *args, **kwargs ) :
         if self.Pipeline.get() == 'initialqcrnaseq' :
             self.om4.grid_forget()
             self.sampleLF.grid_forget()
-            self.info.grid_forget()
+            self.info.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 )
@@ -253,16 +253,19 @@ def makejson(self, *args):
     ##        grp=[]
             cont=[]
             cont_cpm_cutoff=[]
+            cont_mincount=[]
     ##        lbl=[]
             for x in f:
                   xsplit=x.split()
-                  if len(xsplit) == 3:
+                  if len(xsplit) == 4:
                      cont.append(xsplit[0])
                      cont.append(xsplit[1])
                      cont_cpm_cutoff.append(xsplit[2])
+                     cont_mincount.append(xsplit[3])
 
             D["rcontrasts"]=cont
             D["rcontrasts_cpm_cutoff"]=cont_cpm_cutoff
+            D["rcontrasts_min_counts"]=cont_mincount
     #        contrasts["rcontrasts"]=cont
             contrasts=D
         except: