Merge pull request #19 from galaxy-genome-annotation/expression_fix

Fix loading of expression data when first column header is not empty

Author: abretaud

README.md

@@ -87,6 +87,9 @@ $ chakin feature load_fasta \
 
 ## History
 
+- 2.3.7
+    - Fix loading of expression data when first column header is not empty
+
 - 2.3.6
     - Fix loading of GO terms from GFF
 

chado/expression/__init__.py

@@ -584,10 +584,11 @@ def _process_matrix_file(self, file_path, separator):
             with open(file_path) as f:
                 reader = csv.reader(f, delimiter=separator)
                 # Get headers (biomat list)
-                # TODO : python2 compat (reader.next())
-                biomaterial__full_list = next(reader)
+                biomaterial_full_list = next(reader)
+                # Remove first col (=transcript ids)
+                biomaterial_full_list = biomaterial_full_list[1:]
                 # Cleanup empty strings
-                biomaterial_list = [x for x in biomaterial__full_list if x]
+                biomaterial_list = [x for x in biomaterial_full_list if x]
                 expected_len = len(biomaterial_list)
                 for line in reader:
                     # Get feature name

setup.py

@@ -6,7 +6,7 @@
 
 setup(
     name="chado",
-    version='2.3.6',
+    version='2.3.7',
     description="Chado library",
     author="Anthony Bretaudeau",
     author_email="anthony.bretaudeau@inrae.fr",

test-data/expression_title.matrix

@@ -0,0 +1,4 @@
+transcript	Biomat1	Biomat2	Biomat3	Biomat4	Biomat5	Biomat6	Biomat7	Biomat8	
+Q02123|VNBP_POPMV	0.01	0.02	0.06	0.08	1.11111	1.21	1.98	1.88855
+P16654|VNBP_PVSP	2.68	9.84	2.65	4.2	0	0.2	85.1	1.0
+Q00572|VNBP_HELVS	2.01	2.5	1.1	8.65	50.0	0	1.6	9

test/expression_test.py

@@ -76,6 +76,28 @@ def test_add_expression(self):
 
         assert elements.count() == 24
 
+    def test_add_expression_title(self):
+
+        # Setup testing data
+        # Expression file
+        expression_file_path = "./test-data/expression_title.matrix"
+
+        org = self._create_fake_org()
+        an = self._create_fake_an()
+
+        # Feature file (fasta)
+        feature_file_path = "./test-data/proteins.fa"
+        self.ci.feature.load_fasta(fasta=feature_file_path, analysis_id=an['analysis_id'], organism_id=org['organism_id'], sequence_type='mRNA')
+        self.ci.expression.add_expression(org['organism_id'], an['analysis_id'], expression_file_path, separator="\t")
+
+        biomat_list = self.ci.expression.get_biomaterials()
+        assert len(biomat_list) == 8, "Unexpected number of biomaterials created"
+
+        elements = self.ci.session.query(self.ci.model.element.arraydesign_id, self.ci.model.elementresult.quantification_id, self.ci.model.elementresult.signal) \
+            .join(self.ci.model.elementresult, self.ci.model.element.element_id == self.ci.model.elementresult.element_id)
+
+        assert elements.count() == 24
+
     def setUp(self):
 
         self.ci = ci