From 4e34a884c151dd3089e4c0c407c689f0ce1965d4 Mon Sep 17 00:00:00 2001
From: anastasiia <anastasiia.petrova@mpi-bn.mpg.de>
Date: Wed, 14 Nov 2018 16:05:01 +0100
Subject: [PATCH] looking for genes of interest in the genes gtf file

---
 find_exons.py | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/find_exons.py b/find_exons.py
index dd87554..c09bec6 100644
--- a/find_exons.py
+++ b/find_exons.py
@@ -24,6 +24,8 @@
 import random
 import textwrap
 
+#from gtfparse import read_gtf #makes the logger to look different o_o
+
 logger = logging.getLogger('find_exons')
 logger.setLevel(logging.INFO)
 
@@ -102,6 +104,40 @@ 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"])
+
+	all_genes = {}
+
+	#first look for the genew in the gtf_genes file
+	for i in range(len(genes_of_interest)):
+		gene_name = genes_of_interest[i]
+		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()
+
+	#print()
+	for gene in all_genes:
+		print(gene)
+
 def main():
 
 	start = time.time()
@@ -130,6 +166,8 @@ 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)
+
 	logger.info("find_exons needed %s seconds to generate the output" % (time.time() - start))
 	
 	for handler in logger.handlers: