changed test_generate_symbolic_allele

Author: khetherin

tests/test_vcfline.py

@@ -102,10 +102,10 @@ def test_generate_symbolic_allele(self):
                                                                        self.all_possible_lines_dictionary,
                                                                        self.reference_lookup.symbolic_allele_dictionary)
         assert output_symbolic_allele == '<DEL>'
-        print(info_field)
         assert info_field == {'END': '78', 'IMPRECISE': None, 'CIPOS': None, 'CIEND': None, 'SVLEN': '1'}
-        assert output_lines_standard_alt == ['##ALT=<ID=DEL,Description="Deletion">', '##ALT=<ID=DEL,Description="Deletion">']
-        assert output_lines_standard_info == ['##INFO=<ID=ID,Number=.,Type=String,Description="A unique identifier">', '##INFO=<ID=NAME,Number=.,Type=String,Description="Name">', '##INFO=<ID=ALIAS,Number=.,Type=String,Description="Secondary Name">', '##INFO=<ID=VARCALLSOID,Number=.,Type=String,Description="Variant call Sequence ontology ID">', '##INFO=<ID=SVCID,Number=.,Type=Integer,Description="submitter variant call ID">', '##INFO=<ID=REMAP,Number=.,Type=Float,Description="Remap score">', '##INFO=<ID=VARSEQ,Number=.,Type=String,Description="Alleles found in an individual (or group of individuals).">', '##INFO=<ID=END,Number=1,Type=Integer,Description="End position on CHROM (used with symbolic alleles; see below) or End position of the longest variant described in this record">', '##INFO=<ID=SVLEN,Number=A,Type=String,Description="Length of structural variant">', '##INFO=<ID=END,Number=1,Type=Integer,Description="End position on CHROM (used with symbolic alleles; see below) or End position of the longest variant described in this record">', '##INFO=<ID=SVLEN,Number=A,Type=String,Description="Length of structural variant">']
+        assert output_lines_standard_alt == ['##ALT=<ID=DEL,Description="Deletion">', '##ALT=<ID=DEL,Description="Deletion">', '##ALT=<ID=DEL,Description="Deletion">']
+        assert output_lines_standard_info == ['##INFO=<ID=ID,Number=.,Type=String,Description="A unique identifier">', '##INFO=<ID=NAME,Number=.,Type=String,Description="Name">', '##INFO=<ID=ALIAS,Number=.,Type=String,Description="Secondary Name">', '##INFO=<ID=VARCALLSOID,Number=.,Type=String,Description="Variant call Sequence ontology ID">', '##INFO=<ID=SVCID,Number=.,Type=Integer,Description="submitter variant call ID">', '##INFO=<ID=REMAP,Number=.,Type=Float,Description="Remap score">', '##INFO=<ID=VARSEQ,Number=.,Type=String,Description="Alleles found in an individual (or group of individuals).">', '##INFO=<ID=END,Number=1,Type=Integer,Description="End position on CHROM (used with symbolic alleles; see below) or End position of the longest variant described in this record">', '##INFO=<ID=SVLEN,Number=A,Type=String,Description="Length of structural variant">', '##INFO=<ID=ID,Number=.,Type=String,Description="A unique identifier">', '##INFO=<ID=NAME,Number=.,Type=String,Description="Name">', '##INFO=<ID=ALIAS,Number=.,Type=String,Description="Secondary Name">', '##INFO=<ID=VARCALLSOID,Number=.,Type=String,Description="Variant call Sequence ontology ID">', '##INFO=<ID=SVCID,Number=.,Type=Integer,Description="submitter variant call ID">', '##INFO=<ID=REMAP,Number=.,Type=Float,Description="Remap score">', '##INFO=<ID=VARSEQ,Number=.,Type=String,Description="Alleles found in an individual (or group of individuals).">', '##INFO=<ID=END,Number=1,Type=Integer,Description="End position on CHROM (used with symbolic alleles; see below) or End position of the longest variant described in this record">', '##INFO=<ID=SVLEN,Number=A,Type=String,Description="Length of structural variant">', '##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">', '##INFO=<ID=CIPOS,Number=.,Type=Integer,Description="Confidence interval around POS for symbolic structural variants">', '##INFO=<ID=CIEND,Number=.,Type=Integer,Description="Confidence interval around END for symbolic structural variants">', '##INFO=<ID=END,Number=1,Type=Integer,Description="End position on CHROM (used with symbolic alleles; see below) or End position of the longest variant described in this record">', '##INFO=<ID=SVLEN,Number=A,Type=String,Description="Length of structural variant">']
+
 
     def test_get_alt(self):
         alt_allele = self.v.get_alt(self.standard_lines_dictionary, self.all_possible_lines_dictionary, self.reference_lookup)