updated

galaxy-genome-annotation · Jun 11, 2020 · 26cae6e · 26cae6e
1 parent cf971b4
commit 26cae6e
Show file tree

Hide file tree

Showing 2 changed files with 6 additions and 9 deletions.
diff --git a/test-data/gene-top.gff b/test-data/gene-top.gff
@@ -1,10 +1,5 @@
 ##gff-version	3
 ##sequence-region	Merlin	1	172788
-ctg123	example	gene	1050	9000	.	+	.	ID=EDEN;Name=EDEN;Note=protein	kinase
-ctg123	example	mRNA	1050	9000	.	+	.	ID=EDEN.1;Parent=EDEN;Name=EDEN.1;Index=1
-ctg123	example	five_prime_UTR	1050	1200	.	+	.	Parent=EDEN.1
-ctg123	example	CDS	1201	1500	.	+	0	Parent=EDEN.1
-ctg123	example	CDS	3000	3902	.	+	0	Parent=EDEN.1
-ctg123	example	CDS	5000	5500	.	+	0	Parent=EDEN.1
-ctg123	example	CDS	7000	7608	.	+	0	Parent=EDEN.1
-ctg123	example	three_prime_UTR	7609	9000	.	+	.	Parent=EDEN.1
+Merlin	GeneMark.hmm	mRNA	2	691	.	+	.	ID=Merlin_1_mRNA;Parent=Merlin_1;seqid=Merlin;color=#00ff00
+Merlin	GeneMark.hmm	exon	2	691	.	+	.	ID=Merlin_1_exon;Parent=Merlin_1_mRNA;seqid=Merlin
+Merlin	GeneMark.hmm	CDS	2	691	.	+	0	ID=Merlin_1_CDS;Parent=Merlin_1_mRNA;seqid=Merlin
diff --git a/test/annotations_test.py b/test/annotations_test.py
@@ -9,7 +9,9 @@
 def parse(path):
     in_handle = open(path)
     for rec in GFF.parse(in_handle):
-        yield rec
+        print("rec -> "+str(rec)+"\n")
+        for f in rec.features:
+            print("feature ->" + str(f)+"\n")
 
 
 class AnnotationsTest(ApolloTestCase):