the extracting of information from the gtf files is done

find_exons.py

@@ -104,49 +104,56 @@ def check_existing_input_files(args):
 
 	return args.genes
 
-def procede_gtf(gtf_genes, gtf_exons, genes_of_interest, output_directory):
-	#df = read_gtf(gtf_genes)
-	#df_genes = df[df["feature"] == "gene"][df["gene_name"] == genes_of_interest[0]]
-	#print(df_genes)
-	#print(df_genes["seqname"], df_genes["source"], df_genes["feature"], df_genes["start"], df_genes["end"])
+def procede_gtf_files(gtf_genes, gtf_exons, genes_of_interest):
 
 	all_genes = {}
 
-	#first look for the genew in the gtf_genes file
 	for gene_name in genes_of_interest:
-		print(gene_name)
+		#first look for the genes in the gtf_genes file
 		small_gtf_genes = subprocess.getoutput("grep " + gtf_genes + " -e \"" + gene_name + "\"")#find the first line of the input file
-		#small_gtf_genes_lines = re.split(r'\n', small_gtf_genes)
-		for genes_line in re.split(r'\n', small_gtf_genes):
-			print(line)
-			print()
-
-
-
-		"""
-		with open(gtf_genes) as gtf_genes_file:
-			for line in gtf_genes_file:
-				if gene_name in line:
-					line_array = re.split(r'\t', line.rstrip('\n'))
-					gene_start = int(line_array[3])
-					gene_end = int(line_array[4])
-					attributes = re.split(r'; ', line_array[8])
-					for attribut in attributes:
-						if attribut.startswith("gene_id"):
-							gene_id = re.split(r'\s', attribut)[1].replace('"', '')
-						elif attribut.startswith("gene_name"):
-							gene_full_name = re.split(r'\s', attribut)[1].replace('"', '')
-					gene_length = gene_end - gene_start
-	
-					all_genes[gene_full_name] = all_genes.get(gene_full_name, {})
-					all_genes[gene_full_name] = {'gene_start': gene_start, 'gene_end': gene_end, 'gene_length': gene_length, 'gene_id': gene_id}
 
-		gtf_genes_file.close()
-		"""
+		for genes_line in re.split(r'\n', small_gtf_genes):
+			genes_array = re.split(r'\t', genes_line)
+			gene_start = int(genes_array[3])
+			gene_end = int(genes_array[4])
+			gene_length = gene_end - gene_start
+			attributes = re.split(r'; ', genes_array[8])
+			for attribut in attributes:
+				if attribut.startswith("gene_name"):
+					gene_full_name = re.split(r'\s', attribut)[1].replace('"', '')
+
+			all_genes[gene_full_name] = all_genes.get(gene_full_name, {})
+			exons = []
+			all_genes[gene_full_name] = {'gene_start': gene_start, 'gene_end': gene_end, 'gene_length': gene_length, 'exons': exons}
+
+		#find the nubmer and the length of all exons for each gene of interest
+		small_gtf_exons = subprocess.getoutput("grep " + gtf_exons + " -e \"" + gene_name + "\"")
+
+		for exons_line in re.split(r'\n', small_gtf_exons):
+			genes_array = re.split(r'\t', exons_line)
+			exon_start = int(genes_array[3])
+			exon_end = int(genes_array[4])
+			attributes = re.split(r'; ', genes_array[8])
+			for attribut in attributes:
+				if attribut.startswith("gene_name"):
+					gene_full_name = re.split(r'\s', attribut)[1].replace('"', '')
+				elif attribut.startswith("exon_number"):
+					exon_number = re.split(r'\s', attribut)[1]
+				elif attribut.startswith("transcript_support_level"):
+					tsl = re.split(r'\s', attribut)[1].replace('"', '') #do not cast on int, because the tsl can also be NA
+
+			if gene_full_name in all_genes.keys():
+				all_genes[gene_full_name]['exons'].append([exon_start, exon_end, exon_number, tsl])
+
+	"""
+	for gene in all_genes:
+		print(gene, all_genes[gene])
+		print()
+	"""
+	return all_genes
+
+def make_plot(all_genes, output_directory):
 
-	#print()
-	#for gene in all_genes:
-	#	print(gene)
 
 def main():
 
@@ -176,7 +183,8 @@ def main():
 	logger.info("find_exons.py was called using these parameters:")
 	logger.info(vars(args))
 
-	procede_gtf(args.gtf_genes, args.gtf_exons, args.genes, args.output_directory)
+	all_genes = procede_gtf_files(args.gtf_genes, args.gtf_exons, args.genes)
+	make_plot(all_genes, args.output_directory)
 
 	logger.info("find_exons needed %s seconds to generate the output" % (time.time() - start))