fixing the bug. now all the genes will be converted to lowercase to e…

…xclude the problems with input files

visualize.py

@@ -156,10 +156,13 @@ def read_correlation(correlation_file, groups, variable):
 
 		for gene_name in genes_of_interest:
 
-			genes_to_show[gene_name] = genes_to_show.get(gene_name, []) #get a place in the dictionary for this gene
+			orig_gene_name = gene_name.lower()
+
+			genes_to_show[orig_gene_name] = genes_to_show.get(orig_gene_name, []) #get a place in the dictionary for this gene
 
 			#first look for the genes in the gtf_genes file
 			genes_family = subprocess.getoutput("grep -i " + gene_name + " " + correlation_file)
+			print(genes_family)
 
 			if len(genes_family) != 0:
 				logger.info("working with the gene " + gene_name)
@@ -168,16 +171,20 @@ def read_correlation(correlation_file, groups, variable):
 
 				for genes_line in re.split(r'\n', genes_family):
 					genes_array = re.split(r'\t', genes_line)
-					if genes_array[0] == gene_name:
+
+					check_gene_name = genes_array[0].lower()
+
+					print(genes_array)
+					if check_gene_name == orig_gene_name:
 						#this is a perfect match <3
-						genes_to_show[gene_name].append(float(genes_array[3])) #append score to the array
-					elif genes_array[0].startswith(gene_name) and len(genes_array[0]) <= len(gene_name) + variable: #the found gene is by default 1 char longer than the gene name
-						if genes_array[0] in genes_to_show.keys():
-							genes_to_show[genes_array[0]].append(float(genes_array[3]))
+						genes_to_show[check_gene_name].append(float(genes_array[3])) #append score to the array
+					elif check_gene_name.startswith(orig_gene_name) and len(genes_array[0]) <= len(gene_name) + variable: #the found gene is by default 1 char longer than the gene name
+						if check_gene_name in genes_to_show.keys():
+							genes_to_show[check_gene_name].append(float(genes_array[3]))
 						else: #this gene is not yet saved
 							#make a new place in the dictionary for this gene
-							genes_to_show[genes_array[0]] = genes_to_show.get(genes_array[0], [])
-							genes_to_show[genes_array[0]].append(float(genes_array[3]))
+							genes_to_show[check_gene_name] = genes_to_show.get(check_gene_name, [])
+							genes_to_show[check_gene_name].append(float(genes_array[3]))
 
 			else:
 				logger.info("no similar genes to " + gene_name + " were found")
@@ -186,6 +193,7 @@ def read_correlation(correlation_file, groups, variable):
 		genes_to_show = dict([(k, v) for k, v in genes_to_show.items() if len(v) > 0])
 		genes_to_show_groups.append(genes_to_show)
 
+	print(genes_to_show_groups)
 	return genes_to_show_groups
 
 def main():