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Fix tests #9

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Merged
tcezard merged 1 commit into from
Oct 15, 2025
Merged

Fix tests #9

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15 changes: 9 additions & 6 deletions convert_gvf_to_vcf/convertGVFtoVCF.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@ def read_file(prefix, header_type):
"""
file_lines = {}
keys_tsv_file = os.path.join(etc_folder, f'{prefix}{header_type}keys.tsv')
print(keys_tsv_file)
try:
with open(keys_tsv_file) as keys_file:
next(keys_file) # Skip the header
Expand All @@ -28,8 +29,9 @@ def read_file(prefix, header_type):
for token in range(number_of_tokens):
value_to_add = file_tokens[token]
file_lines.setdefault(key_id, []).append(value_to_add)
except FileNotFoundError:
except FileNotFoundError as e:
print(f'File not found: {keys_tsv_file}')
raise e
return file_lines


Expand Down Expand Up @@ -206,11 +208,12 @@ def convert_gvf_attributes_to_vcf_values(column9_of_gvf,
# if dgva specific key, create custom string otherwise do standard
if attrib_key in dgva_attribute_dict:
lines_custom_structured.append(
generate_custom_structured_metainformation_line(vcf_key="INFO", vcf_key_id=attrib_key,
vcf_key_number=dgva_attribute_dict[attrib_key][1],
vcf_key_type=dgva_attribute_dict[attrib_key][2],
vcf_key_description=dgva_attribute_dict[attrib_key][3],
optional_extra_fields=None)
generate_custom_structured_metainformation_line(
vcf_key="INFO", vcf_key_id=attrib_key,
vcf_key_number=dgva_attribute_dict[attrib_key][1],
vcf_key_type=dgva_attribute_dict[attrib_key][2],
vcf_key_description=dgva_attribute_dict[attrib_key][3],
optional_extra_fields=None)
)
vcf_vals[attrib_key]=gvf_attribute_dictionary[attrib_key]
elif attrib_key == "allele_count":
Expand Down
1 change: 1 addition & 0 deletions convert_gvf_to_vcf/etc/reservedFILTERkeys.tsv
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@@ -0,0 +1 @@
Key Number Type Description
0 ...ert_gvf_to_vcf/etc/ReservedFORMATkeys.tsv → ...ert_gvf_to_vcf/etc/reservedFORMATkeys.tsv
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0 convert_gvf_to_vcf/etc/ReservedINFOkeys.tsv → convert_gvf_to_vcf/etc/reservedINFOkeys.tsv
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1 change: 1 addition & 0 deletions convert_gvf_to_vcf/etc/svFILTERkeys.tsv
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@@ -0,0 +1 @@
KEY LINE