germline/tests: Test split-from-imgt.py

We use this for reorganizing where tests are launched

.gitlab-ci.yml

@@ -45,7 +45,7 @@ test_germlines:
   stage: test_germlines
   script:
     - make -C germline get-all-data
-    - make -C germline/tests
+    - make -C germline tests
   only:
     - /^feature-.*g.*\/.*$/
 

germline/Makefile

@@ -30,7 +30,12 @@ diff-from-saved:
 	echo
 	diff -r -u -x "*[.][^f][^a]" -x "germline*" -x "get*" -x "Makefile" -x "saved-*" saved-germline/ .
 
+tests:
+	python split-from-imgt.py --test
+	make -C tests
+
+
 distrib: get-all-data js
 	cd .. ; tar cvzf germline-`cat germline/germline_id`.tar.gz germline/germline_id germline/*/*.fa germline/IMGT_RELEASE browser/js/germline.js
 
-.PHONY: all germline js get-all-data clean diff-from-saved
+.PHONY: all germline js get-all-data clean diff-from-saved tests

germline/split-from-imgt.py

@@ -75,7 +75,7 @@ def get_gene_coord(imgt_line):
     >>> line = '>X15272|TRGV4*01|Homo sapiens|F|V-REGION|406..705|300 nt|1| | | | |300+0=300| |rev-compl|'
     >>> get_gene_coord(line)[0] == 'X15272'
     True
-    >>> get_gene_coord(line)[1] == {'from': 406, 'to': 705, 'imgt_data': 'TRGV4*01|Homo sapiens|F|V-REGION', 'imgt_name': 'TRGV4*01'}
+    >>> get_gene_coord(line)[1] == {'from': 406, 'to': 705, 'imgt_data': 'TRGV4*01|Homo sapiens|F|V-REGION', 'imgt_name': 'TRGV4*01', 'species': 'Homo sapiens'}
     True
     '''
     elements = imgt_line.split('|')
@@ -338,6 +338,10 @@ def split_IMGTGENEDBReferenceSequences(f, gene_list):
 
 if __name__ == '__main__':
 
+    if sys.argv[1] == '--test':
+        import doctest
+        doctest.testmod()
+    else:
         print (IMGT_LICENSE)
 
         ReferenceSequences = sys.argv[1]