Fix tests

Author: tcezard

convert_gvf_to_vcf/etc/svALTkeys.tsv

@@ -1,12 +1,12 @@
 KEY	LINE
-INV    ##ALT=<ID=INV,Description="Inversion">
-INS    ##ALT=<ID=INS,Description="Insertion">
-DUP    ##ALT=<ID=DUP,Description="Duplication">
-DEL    ##ALT=<ID=DEL,Description="Deletion">
-CNV    ##ALT=<ID=CNV,Description="Copy number variable region">
-CNV:TR    ##ALT=<ID=CNV:TR,Description="Tandem repeat determined based on DNA abundance">
-DUP:TANDEM    ##ALT=<ID=DUP:TANDEM,Description="Tandem duplication">
-DEL:ME    ##ALT=<ID=DEL:ME,Description="Deletion of mobile element relative to the reference">
-INS:ME    ##ALT=<ID=INS:ME,Description="Insertion of mobile element relative to the reference">
-R    ##ALT=<ID=R,Description="IUPAC code R = A/G">
-M    ##ALT=<ID=M,Description="IUPAC code M = A/C">
+INV	##ALT=<ID=INV,Description="Inversion">
+INS	##ALT=<ID=INS,Description="Insertion">
+DUP	##ALT=<ID=DUP,Description="Duplication">
+DEL	##ALT=<ID=DEL,Description="Deletion">
+CNV	##ALT=<ID=CNV,Description="Copy number variable region">
+CNV:TR	##ALT=<ID=CNV:TR,Description="Tandem repeat determined based on DNA abundance">
+DUP:TANDEM	##ALT=<ID=DUP:TANDEM,Description="Tandem duplication">
+DEL:ME	##ALT=<ID=DEL:ME,Description="Deletion of mobile element relative to the reference">
+INS:ME	##ALT=<ID=INS:ME,Description="Insertion of mobile element relative to the reference">
+R	##ALT=<ID=R,Description="IUPAC code R = A/G">
+M	##ALT=<ID=M,Description="IUPAC code M = A/C">

requirements.txt

@@ -1 +1,2 @@
 ebi_eva_common_pyutils >= 0.7.4, == 0.*
+biopython

tests/test_convert_gvf_to_vcf.py

@@ -125,6 +125,7 @@ def test_generate_vcf_metainformation(self):
         vcf_data_lines, list_of_vcf_objects = gvf_features_to_vcf_objects(gvf_lines_obj_list,
                                                                           dgva_attribute_dict,
                                                                           gvf_attribute_dict,
+                                                                          self.assembly,
                                                                           lines_custom_structured,
                                                                           lines_standard_ALT,
                                                                           lines_standard_INFO,
@@ -276,7 +277,6 @@ def test_format_sample_values(self):
         all_possible_ALT_lines = generate_all_possible_standard_structured_alt_lines()
         all_possible_FILTER_lines = generate_all_possible_standard_structured_filter_lines()
         all_possible_FORMAT_lines = generate_all_possible_standard_structured_format_lines()
-
         vcf_data_lines, list_of_vcf_objects = gvf_features_to_vcf_objects(gvf_lines_obj_list,
                                                                           dgva_attribute_dict,
                                                                           gvf_attribute_dict,