here for some text
- n_samples=0
- for sample in stat_dict.iterkeys():
- n_samples+=1
- rval.append("
"%(sample))
+ rval.append("
")
curr_dir = os.path.dirname(os.path.realpath(__file__))
shutil.copy(os.path.join(curr_dir,"jquery-1.10.2.min.js"),directory)
shutil.copy(os.path.join(curr_dir,"jqBarGraph.2.1.js"),directory)
rval.append("")
rval.append("")
- rval.append('")
rval.append( '' )
with open(file,'w') as file:
file.write("\n".join( rval ))
-def transformDict(stat_dict):
- dict={}
- position={}
- dict_label={}
- for sample in stat_dict.iterkeys():
- dict[sample]=[{},{}]
- position[sample]={}
- dict_label[sample]={}
- j=0
- for family in stat_dict[sample].iterkeys():
-
- i=0
- for region,values in stat_dict[sample][family].iteritems():
-
- if i not in dict[sample][0]:
- dict[sample][0][i]=[]
- dict[sample][1][i]=[]
- position[sample][i]=[]
- dict_label[sample][i]=[]
- dict[sample][0][i].append(int(values[0][1]))
- dict[sample][1][i].append(int(values[0][2]))
- position[sample][i].append(j)
- dict_label[sample][i].append(values[0][0])
- i+=1
- j+=1
- return dict,position,dict_label
def customeLegend(color_map):
legend_map=[[],[]]
- for label in color_map:
- box=Rectangle((0,0),1,1,color=color_map[label],fill=True)
- legend_map[0].append(box)
- legend_map[1].append(label)
- plt.figlegend(legend_map[0],legend_map[1],loc=8,ncol=len(color_map))
+ for sample in color_map:
+ legend_map[0].append(Rectangle((0,0),0,0,visible=False))
+ legend_map[1].append(sample)
+ for label in color_map[sample]:
+ box=Rectangle((0,0),1,1,color=color_map[sample][label],fill=True)
+ legend_map[0].append(box)
+ legend_map[1].append(label)
+ plt.figlegend(legend_map[0],legend_map[1],loc=9,ncol=len(color_map),prop={'size':8})
def generatePyPlot(stat_dict,output_file):
pp = PdfPages(output_file)
- fig = plt.figure()
-
- n_samples=len(stat_dict)
- dict,position,dict_label=transformDict(stat_dict)
+
+ color_map=rgb_color_variants(stat_dict)
+ n_samples=len(color_map)
+ for plot in ["reads","bp"]:
+ fig=plt.figure()
+ i=0
+ for f,fam in stat_dict.iteritems():
+ j=0
+ for s,sample in fam.samples.iteritems():
+ values = []
+ color = []
+ for r,region in sample.regions.iteritems():
+ values.append(int(getattr(region,plot)))
+ color.append(color_map[s][region.state])
+ if(len(values)>1):
+ b = values[:-1]
+ b.insert(0,0);
+ for u in range(1,len(b)):
+ b[u]+=b[u-1]
+ plt.bar([i+j]*len(values),values,bottom=b,width=0.8,color=color)
+ else:
+ plt.bar([i+j]*len(values),values,width=0.8,color=color)
- i=0
- for sample in dict.iterkeys():
- fig = plt.figure()
-
- fig.subplots_adjust(bottom=0.25,hspace=0.5)
-
- r,g,b,a=cm.hsv(1.*(1-(i/n_samples)))
- color_map=rgb_color_variants(r,g,b)
-
- for sub in [0,1]:
- plt.subplot(1,2,sub+1)
- bottom={}
- for level,values in dict[sample][sub].iteritems():
- colors=[color_map[r] for r in dict_label[sample][level]]
-
- if level==0:
-
- plt.bar(position[sample][level],values,bottom=0, width=0.8 ,color=colors)
- else:
- lastvalues=[]
- for oldpos in range(len(values)):
- lastvalues.append(bottom[position[sample][level][oldpos]])
-
- plt.bar(position[sample][level],values, width=0.8,bottom=lastvalues ,color=colors)
- for pos in range(len(values)):
- if position[sample][level][pos] not in bottom:
- bottom[position[sample][level][pos]]=values[pos]
- else:
- bottom[position[sample][level][pos]]+=values[pos]
- pos=[x+0.4 for x in range(len(stat_dict[sample]))]
- plt.xticks(pos, stat_dict[sample].keys(), rotation='vertical')
- if(sub==0):
+ j+=1
+ i+= 1+n_samples
+ pos=[means(x,x+n_samples)+0.4 for x in arange(0,i+n_samples,1+n_samples)]
+ plt.xticks(pos, stat_dict.keys(), rotation='vertical')
+ if(plot=="reads"):
plt.ylabel("Cumulative reads assigned to family")
- else:
+ if(plot=="bp"):
plt.ylabel("Cumulative basepairs assigned to family")
- plt.xlabel("")
- fig.subplots_adjust(bottom=0.25,wspace=0.5)
- remove_border()
+ plt.xlabel("")
+ fig.subplots_adjust(bottom=0.25,wspace=0.5,top=0.8)
+ remove_border()
customeLegend(color_map)
- plt.suptitle(sample)
pp.savefig(fig)
- i+=1
pp.close()
-def parseStatFile(filename):
+def parseStatFile(filename, directory):
with open(filename,'r') as file:
values=[ map(str,line.split('\t')) for line in file ]
- dict={}
+ family_dict={}
for line in values[1:]:
- if line[3] not in dict:
- dict[line[3]]={}
- dict[line[3]][line[1]]={}
- dict[line[3]][line[1]][line[2]]=[[line[4],line[5],line[7],line[0],line[6]]]
- else:
- if line[1] not in dict[line[3]]:
- dict[line[3]][line[1]]={}
- dict[line[3]][line[1]][line[2]]=[[line[4],line[5],line[7],line[0],line[6]]]
- else:
- if line[2] not in dict[line[3]][line[1]]:
- dict[line[3]][line[1]][line[2]]=[[line[4],line[5],line[7],line[0],line[6]]]
- else:
- dict[line[3]][line[1]][line[2]].append([line[4],line[5],line[7],line[0],line[6]])
-# for key in dict.iterkeys():
-# for family_key,values in dict[key].iteritems():
-# for line in values:
-# print key,family_key,line
- return dict
-def getFiles(directory):
- rval={}
- dlist = os.listdir(directory)
- for dire in dlist:
- if(os.path.isdir(os.path.join(directory,dire))):
- rval[dire]={}
- flist = os.listdir(os.path.join(directory,dire))
- for file in flist:
- split=file.split("_")
- region=split[1]
- if region not in rval[dire]:
- rval[dire][region]=[file]
- else:
- rval[dire][region].append(file)
-
- return rval
+ fam_type,fam,region,sample,state,reads,length,bp,coverage=line
+ if fam not in family_dict:
+ family= Family(fam,fam_type,directory=directory)
+ family_dict[fam]=family
+ family_dict[fam].add(sample,region,state,reads,bp,length)
+
+ return family_dict
+
+class Family:
+
+ def __init__(self,name,typ,directory=None,samples=None):
+ self.name=name
+ if samples!=None:
+ self.samples=samples
+ else:
+ self.samples={}
+ self.directory=directory
+ self.typ=typ
+ if self.directory:
+ self.files=self.__getFiles(directory)
+ else:
+ self.files=None
+
+ def add(self,sample,region,state,reads,bp,length):
+ if sample not in self.samples:
+ s = Sample(sample)
+ self.samples[sample]=s
+
+ return self.samples[sample].add(region,state,reads,bp,self.files[region],length)
+ def __getFiles(self,directory):
+ dlist = os.listdir(os.path.join(directory,self.typ+"_"+self.name))
+ dict={}
+ for file in dlist:
+ try:
+ wc,region,suf = file.split("_")
+ except ValueError:
+ continue
+ if region not in dict:
+ dict[region]={}
+ dict[region][suf]=file #bit redundant?! just save TRUE or FALSE?
+ return dict
+
+ def __str__(self):
+ return "{'type':'%s', 'samples':%s}"%(self.typ,str(self.samples))
+
+ def __repr__(self):
+ return "{'type':'%s', 'samples':%s}"%(self.typ,str(self.samples))
+
+class Sample:
+
+ def __init__(self,name,regions=None):
+ self.name=name
+ if regions!=None:
+ self.regions=regions
+ else:
+ self.regions={}
+ def add(self,region,state,reads,bp,files,length):
+ if region not in self.regions:
+ r = Region(region,state,reads,bp,files,length)
+ self.regions[region]=r
+ return True
+ else:
+ return False
+
+ def __str__(self):
+ return str(self.regions)
+
+ def __repr__(self):
+ return str(self.regions)
+
+
+class Region:
+
+ def __init__(self,id,state,reads,bp,files,length):
+ self.id=id
+ self.state=state
+ self.reads=reads
+ self.bp=bp
+ self.files=files
+ self.length=length
+
+ def __str__(self):
+ return "{'state':'%s', 'reads':%s, 'bp':%s, 'files':%s, 'length':%s}" %(self.state,self.reads,self.bp,self.files,self.length)
+
+ def __repr__(self):
+ return "{'state':'%s', 'reads':%s, 'bp':%s, 'files':%s, 'length':%s}" %(self.state,self.reads,self.bp,self.files,self.length)
+
if __name__ == "__main__":
@@ -274,9 +300,10 @@
args.insert(0,"dummy")
try:
- RegionRunner.run(argv=args)
+ sys.exit(1)#RegionRunner.run(argv=args)
except SystemExit:
- stat_dict=parseStatFile(options.stat_file)
+ stat_dict=parseStatFile(options.stat_file,options.directory)
+
generatePyPlot(stat_dict,os.path.join(options.directory,"plot.pdf"))
generateHTML(stat_dict,options.html_file,options.directory)