to not loose some of the genes while looking for transcripts we are s…

…aving the combination of gene and transcript name

find_exons.py

@@ -312,8 +312,9 @@ def plot_and_output(all_genes, output_directory, gene_groups):
 			if sorted_exons[i][5] != transcript_name or i == len(sorted_exons) - 1: #this is a new transcript or the last one
 				#save the previous transcript_name
 				score = "%.2f" % round((sum_length * 100)/all_genes[gene]['gene_length'], 2)
-				genes_with_transcript_names[transcript_name] = genes_with_transcript_names.get(transcript_name, {})
-				genes_with_transcript_names[transcript_name] = {'gene': gene, 'sum_length': sum_length, 'gene_length': all_genes[gene]['gene_length'], 'score': score}
+				gene_transcript_name = gene + "_" + transcript_name
+				genes_with_transcript_names[gene_transcript_name] = genes_with_transcript_names.get(transcript_name, {})
+				genes_with_transcript_names[gene_transcript_name] = {'gene': gene, 'sum_length': sum_length, 'gene_length': all_genes[gene]['gene_length'], 'score': score}
 				transcript_name = sorted_exons[i][5]
 				sum_length = sorted_exons[i][0]
 			else: #this is still the same transcript name
@@ -369,7 +370,7 @@ def plot_and_output(all_genes, output_directory, gene_groups):
 		#print("i am saving this gene ", all_genes[gene_to_save])
 	"""
 	#sorted_dict = sorted(dict_motifs_p_values.items(), key = lambda x : (x[1]['adjusted_p_value']), reverse = False)
-	
+
 	genes_with_transcript_names = sorted(genes_with_transcript_names.items(), key = lambda x: (x[1]['gene'], x[0]))
 
 	logger.info("writing the output file")
@@ -385,7 +386,7 @@ def plot_and_output(all_genes, output_directory, gene_groups):
 	"""
 
 	for transcript in genes_with_transcript_names:
-		output_file.write('\t'.join([transcript[1]['gene'], transcript[0], str(transcript[1]['score']),str(transcript[1]['gene_length']), str(transcript[1]['sum_length'])]) + '\n')
+		output_file.write('\t'.join([transcript[1]['gene'], transcript[0].replace(transcript[1]['gene'] + '_', ''), str(transcript[1]['score']),str(transcript[1]['gene_length']), str(transcript[1]['sum_length'])]) + '\n')
 
 	output_file.close()