diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 4f1311ce52822cce7ad17c8dbd8da4ebca44b251..79b9a2f13a6014bca16a96054eba160bd8288049 100644 --- a/.gitlab-ci.yml +++ b/.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.*\/.*$/ diff --git a/germline/Makefile b/germline/Makefile index 639334ffb92ad2f80c2d1e2a0fb3b297327fe269..ec3f0dba37b7ad42f073716cf880e147ef22967c 100644 --- a/germline/Makefile +++ b/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 diff --git a/germline/split-from-imgt.py b/germline/split-from-imgt.py index e45187a61326f3788f3eb2134b9b9a3ec87ff50f..37f13d000dde02037e1144686195d3dd965a2136 100644 --- a/germline/split-from-imgt.py +++ b/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('|') @@ -338,11 +338,15 @@ def split_IMGTGENEDBReferenceSequences(f, gene_list): if __name__ == '__main__': - print (IMGT_LICENSE) + if sys.argv[1] == '--test': + import doctest + doctest.testmod() + else: + print (IMGT_LICENSE) - ReferenceSequences = sys.argv[1] - GeneList = sys.argv[2] + ReferenceSequences = sys.argv[1] + GeneList = sys.argv[2] - gl = IMGTGENEDBGeneList(GeneList) - split_IMGTGENEDBReferenceSequences(ReferenceSequences, gl) + gl = IMGTGENEDBGeneList(GeneList) + split_IMGTGENEDBReferenceSequences(ReferenceSequences, gl)