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Merged
tcezard merged 2 commits into from
Dec 2, 2025
Merged

Split VCF line in builder and storage object #18

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fbeb5f5
Split VCF line into a line builder and an object to hold the line
tcezard Dec 1, 2025
14f4fae
Update tests
tcezard Dec 1, 2025
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83 changes: 31 additions & 52 deletions convert_gvf_to_vcf/convertGVFtoVCF.py
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
import argparse
import os
from convert_gvf_to_vcf.utils import read_pragma_mapper, read_in_gvf_file
from convert_gvf_to_vcf.vcfline import VcfLine
from convert_gvf_to_vcf.vcfline import VcfLineBuilder
from convert_gvf_to_vcf.logger import set_up_logging, logger
from convert_gvf_to_vcf.lookup import Lookup
# setting up paths to useful directories
Expand Down Expand Up @@ -48,14 +48,10 @@ def generate_vcf_header_unstructured_line(vcf_unstructured_key,
return custom_unstructured_string

def generate_vcf_header_metainfo(gvf_pragmas,
gvf_non_essential,
list_of_vcf_objects,
standard_lines_dictionary):
gvf_non_essential):
""" Generates a list of metainformation lines for the VCF header
:param gvf_pragmas: list of gvf pragmas to convert
:param gvf_non_essential: list of non-essential gvf pragmas to convert
:param list_of_vcf_objects: list of vcf objects
:param standard_lines_dictionary: dictionary of standard lines
:return: unique_pragmas_to_add, sample_names: a list of pragmas (removed duplicates), list of sample names
"""
pragmas_to_add = []
Expand All @@ -76,8 +72,9 @@ def generate_vcf_header_metainfo(gvf_pragmas,
for pragma in gvf_pragmas:
vcf_header_key, pragma_name, pragma_value = get_pragma_name_and_value(pragma, " ", list_of_pragma, pragma_to_vcf_map)
pragmas_to_add.append(generate_vcf_header_unstructured_line(vcf_header_key, pragma_value))
for vcf_obj in list_of_vcf_objects:
pragmas_to_add.append(generate_vcf_header_unstructured_line("source", vcf_obj.source))
# FIXME: Why are we adding header from the VCF lines
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@khetherin khetherin Dec 1, 2025

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Adding the source (displayed in VCF header as: ##source=DGVa). This comes from the GVF feature line. Alsopragmas_to_add is probably a misleading name, these were GVF pragmas that have been converted to VCF header.

# for vcf_obj in list_of_vcf_objects:
# pragmas_to_add.append(generate_vcf_header_unstructured_line("source", vcf_obj.source))
####
####
# Go through non-essential pragmas
Expand Down Expand Up @@ -112,10 +109,11 @@ def generate_vcf_header_metainfo(gvf_pragmas,
uniq_sample_name.append(sample)
###
unique_pragmas_to_add = list(dict.fromkeys(pragma for pragma in pragmas_to_add if pragma not in unique_pragmas_to_add))
unique_alt_lines_to_add = list(dict.fromkeys(alt_line for alt_line in standard_lines_dictionary["ALT"] if alt_line not in unique_alt_lines_to_add))
unique_info_lines_to_add = list(dict.fromkeys(info_line for info_line in standard_lines_dictionary["INFO"] if info_line not in unique_info_lines_to_add))
unique_filter_lines_to_add = list(dict.fromkeys(filter_line for filter_line in standard_lines_dictionary["FILTER"] if filter_line not in unique_filter_lines_to_add))
unique_format_lines_to_add = list(dict.fromkeys(format_line for format_line in standard_lines_dictionary["FORMAT"] if format_line not in unique_format_lines_to_add))
# TODO: The addition of headers from the VCF lines should be done in the VCF builder
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@khetherin khetherin Dec 1, 2025

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I agree with the TODO. I also think the function generate_vcf_header_metainfo could be simplified.

# unique_alt_lines_to_add = list(dict.fromkeys(alt_line for alt_line in standard_lines_dictionary["ALT"] if alt_line not in unique_alt_lines_to_add))
# unique_info_lines_to_add = list(dict.fromkeys(info_line for info_line in standard_lines_dictionary["INFO"] if info_line not in unique_info_lines_to_add))
# unique_filter_lines_to_add = list(dict.fromkeys(filter_line for filter_line in standard_lines_dictionary["FILTER"] if filter_line not in unique_filter_lines_to_add))
# unique_format_lines_to_add = list(dict.fromkeys(format_line for format_line in standard_lines_dictionary["FORMAT"] if format_line not in unique_format_lines_to_add))

return unique_pragmas_to_add, uniq_sample_name, unique_alt_lines_to_add, unique_info_lines_to_add, unique_filter_lines_to_add, unique_format_lines_to_add

Expand Down Expand Up @@ -182,13 +180,12 @@ def get_pragma_tokens(pragma_value, first_delimiter, second_delimiter):
return pragma_tokens

# This is the main conversion logic
def convert_gvf_features_to_vcf_objects(gvf_lines_obj_list, reference_lookup):
def convert_gvf_features_to_vcf_objects(gvf_lines_obj_list, reference_lookup, ordered_list_of_samples):
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@khetherin khetherin Dec 1, 2025

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Having an ordered_list_of_Samples is a good idea and will be useful in this function. Getting this ordered list will need to come from the GVF pragmas and should be done early on.

""" Creates VCF objects from GVF feature lines and stores the VCF objects.
:param gvf_lines_obj_list: list of GVF feature line objects
:param reference_lookup: an object that stores important dictionaries to be used for reference lookups.
:return: standard_header_lines, vcf_data_lines, list_of_vcf_objects: header lines for this VCF, datalines for this VCF and a list of VCF objects
:return: standard_header_lines, list_of_vcf_objects: header lines for this VCF, datalines for this VCF and a list of VCF objects
"""
vcf_data_lines = {} # DICTIONARY OF LISTS, {Chromosome_Pos: [VCF line object]}
list_of_vcf_objects = []
# Create data structure to store the header lines for this VCF file (standard meta-information lines)
standard_header_lines ={
Expand All @@ -203,27 +200,14 @@ def convert_gvf_features_to_vcf_objects(gvf_lines_obj_list, reference_lookup):
all_header_lines_per_type_dict = {
htype: generate_vcf_header_structured_lines(htype, reference_lookup.mapping_attribute_dict) for htype in ["ALT", "INFO", "FILTER", "FORMAT"]
}

vcf_builder = VcfLineBuilder(standard_header_lines, all_header_lines_per_type_dict, reference_lookup, ordered_list_of_samples)
# Create a vcf object for every feature line in the GVF (1:1)
for gvf_featureline in gvf_lines_obj_list:
#NOTE: this is the main Logic of the code
vcf_object = VcfLine(gvf_featureline,
standard_header_lines,
all_header_lines_per_type_dict,
reference_lookup)
vcf_object = vcf_builder.build_vcf_line(gvf_featureline)
# Store VCF object in the list
list_of_vcf_objects.append(vcf_object)

# vcf_object.key is formatted as follows: Chromosome_Pos
if vcf_object.key in vcf_data_lines:
# Add VCF object to the dictionary of lists
vcf_data_lines[vcf_object.key].append(vcf_object)
else:
# Get it into a format where the VCF object can be added to the dictionary of lists
vcf_data_line_objects_list = [vcf_object]
vcf_data_lines[vcf_object.key] = vcf_data_line_objects_list
# Returns the header of the VCF file, the datalines of the VCF file, and the object.
return standard_header_lines, vcf_data_lines, list_of_vcf_objects
# Returns the header of the VCF file, and the object.
return standard_header_lines, list_of_vcf_objects

# The functions below relate to the VCF objects
def compare_vcf_objects(list_of_vcf_objects):
Expand Down Expand Up @@ -318,32 +302,27 @@ def main():
logger.info(f"Storing the assembly file: {assembly_file}")
logger.info("Storing the IUPAC ambiguity dictionary.")

# Preparation work:
# Store the VCF metainformation and ensure preservation of important GVF data.
# This information will be useful when creating the VCF header.
# TODO: refactor function generate_vcf_metainfo
(
unique_pragmas_to_add,
samples,
unique_alt_lines_to_add,
unique_info_lines_to_add,
unique_filter_lines_to_add,
unique_format_lines_to_add
) = generate_vcf_header_metainfo(gvf_pragmas, gvf_non_essential)

# Convert each feature line in the GVF file to a VCF object (stores all the data for a line in the VCF file).
# NOTE: Main Logic lives here.
(
header_lines,
vcf_data_lines, #TODO: check if this can be removed
list_of_vcf_objects
) = convert_gvf_features_to_vcf_objects(gvf_lines_obj_list, reference_lookup)
(header_lines,list_of_vcf_objects) = convert_gvf_features_to_vcf_objects(gvf_lines_obj_list, reference_lookup, ordered_list_of_samples=samples)

logger.info(f"Writing to the following VCF output: {args.vcf_output}")
logger.info("Generating the VCF header and the meta-information lines")
with open(args.vcf_output, "w") as vcf_output:
# Preparation work:
# Store the VCF metainformation and ensure preservation of important GVF data.
# This information will be useful when creating the VCF header.
# TODO: refactor function generate_vcf_metainfo
(
unique_pragmas_to_add,
samples,
unique_alt_lines_to_add,
unique_info_lines_to_add,
unique_filter_lines_to_add,
unique_format_lines_to_add
) = generate_vcf_header_metainfo(gvf_pragmas,
gvf_non_essential,
list_of_vcf_objects,
header_lines)

logger.info(f"Total number of samples in this VCF: {len(samples)}")

# Part 1 of VCF file: Write the VCF header. This will include perserved data from the GVF file.
Expand Down
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