small refactor / cleanup of old code in get_features

YeoLab · Sep 24, 2014 · 8cec45e · 8cec45e
1 parent a9bde44
commit 8cec45e
Showing 1 changed file with 9 additions and 15 deletions.
diff --git a/clipper/src/get_genomic_regions.py b/clipper/src/get_genomic_regions.py
@@ -356,33 +356,27 @@ def get_feature_locations(self, limit_genes=False, flush_cashe=False):
 
         except ValueError:
             pass
-
-        five_prime_ends = []
-        three_prime_ends = []
-        poly_a_sites = []
-        stop_codons = []
-        start_codons = []
-        transcription_start_sites = []
+
         for i, gene_id in enumerate(self._db.features_of_type('gene')):
             if i % 2000 == 0:
                 print "processed %d genes" % (i)
                 if i == 2000 and limit_genes:
                     break
 
-            gene = { "five_prime_ends" : [],
-                    "three_prime_ends" : [],
-                    "poly_a_sites" : [],
-                    "stop_codons" :  [],
-                    "start_codons" :  [],
-                    "transcription_start_sites" : []}
+            gene = { "five_prime_ends": [],
+                    "three_prime_ends": [],
+                    "poly_a_sites": [],
+                    "stop_codons":  [],
+                    "start_codons":  [],
+                    "transcription_start_sites": []}
             try:
                 for exon in self._db.children(gene_id, featuretype='exon'):
                     exon_start = copy.deepcopy(exon)
                     exon_start.start = exon.start + 1
 
                     exon_stop = copy.deepcopy(exon)
                     exon_stop.start = exon_stop.stop
-                    exon_stop.stop = exon_stop.stop + 1  
+                    exon_stop.stop += 1
 
                     if exon.strand == "-":
                         exon_start, exon_stop = exon_stop, exon_start 
@@ -397,7 +391,7 @@ def get_feature_locations(self, limit_genes=False, flush_cashe=False):
 
                     transcript_stop = copy.deepcopy(transcript)
                     transcript_stop.start = transcript_stop.stop
-                    transcript_stop.stop = transcript_stop.stop + 1
+                    transcript_stop.stop += 1
 
                     if transcript.strand == "-":
                         transcript_start, transcript_stop = transcript_stop, transcript_start