Mergelines by khetherin · Pull Request #15 · EBIvariation/convertGVFtoVCF

khetherin · 2025-11-10T15:27:19Z

No description provided.

convert_gvf_to_vcf/convertGVFtoVCF.py

Major changes to convertGVFtoVCF: - removed compare_and_merge lines and placed functions into VCFlines file Major changes to VCF line: - improved single responsibility principle - added many functions. Function moved from VCFlines to Utils.py (build_iupac_ambiguitycode) New files added: - Lookup.py for referencing - New test files: test_assisting_converter, test_logger, test_utils, test_vcfline (separated out tests to match the file structure) Optimised the function: read_in_gvf_file by removing extraneous for loop

tcezard · 2025-11-21T12:02:20Z

convert_gvf_to_vcf/vcfline.py


-        self.vcf_value, self.info_string, self.format_dict = convert_gvf_attributes_to_vcf_values(gvf_feature_line_object.attributes, mapping_attribute_dict, field_lines_dictionary, all_possible_lines_dictionary)
+        (self.vcf_value, # used to populate the VCF fields. This is a dict of non-converted GVF attribute keys and their values.
+         self.info_string, # a formatted INFO string to form VCF line


You should return and store a info_dict rather than an info_string and leave the formatting the the __str__ function

addressed: strings have been removed

tcezard · 2025-11-21T12:10:54Z

convert_gvf_to_vcf/vcfline.py

This should use the order_format_keys function although I don't thin you should construct the format string here. It should be reserved to the __str__

addressed: used order_format_keys and removed strings

tcezard · 2025-11-21T12:15:06Z

convert_gvf_to_vcf/vcfline.py

+                self.format,
+                self.format_values_by_sample_string


You should not be using stored strings. The should be constructed in this function from the list of format tag and the format_dict.

addressed: removed strings

tcezard · 2025-11-21T12:21:24Z

convert_gvf_to_vcf/vcfline.py

+                self.pos,
+                self.merge_and_add(self.id, other_vcf_line.id, ";"),
+                self.ref,
+                self.merge_and_add(self.alt, other_vcf_line.alt, ","),


What happens if you merge 3 lines. First contains a <DEL>, second contains a <INS> and third contains a <DEL>?

merge('<DEL>', '<INS>') --> '<DEL>,<INS>' merge('<DEL>,<INS>', '<DEL>') --> '<DEL>,<INS>,<DEL>'

not addressed yet

tcezard · 2025-11-21T12:59:16Z

convert_gvf_to_vcf/convertGVFtoVCF.py

+# The functions below relate to the VCF objects
+def compare_vcf_objects(list_of_vcf_objects):
+    """ Compares VCF objects in the list with the VCF object before it. Returns boolean values.
+    :params: list_of_vcf_objects: list of vcf objects
+    :return: comparison_results: list of booleans. For future reference, if True, this will determine merging lines; if False, this will determine use of the previous line.
    """
-    sample_format_value_tokens = []
-    for sample in list_of_sample_names:
-        if sample in sample_name_dict_format_kv:
-            format_value = sample_name_dict_format_kv[sample]
-            sample_format_value_tokens.append(':'.join(format_value.values()))
+    comparison_results = []
+    # For each vcf line object, compare with the previous vcf line object in the list
+    for index in range(1, len(list_of_vcf_objects)):
+        current_vcf_object = list_of_vcf_objects[index]
+        previous_vcf_object = list_of_vcf_objects[index - 1]
+        # Determines the VCF line objects as equal based on the CHROM, POS and REF being the same (__eq__ in Vcfline)
+        if current_vcf_object == previous_vcf_object:
+            comparison_results.append(True) # This will use require merging.
        else:
-            format_value = "." # set to missing value
-            sample_format_value_tokens.append(format_value)
-    sample_format_values_string = '\t'.join(sample_format_value_tokens)
-    return sample_format_values_string
+            comparison_results.append(False) # No merging required. Use previous object.
+    return comparison_results


Calculating the comparison and storing the results seem overly complicated and there are function that exists in python to do what you want.
You should look for itertools.groupby that will probably help

not addressed yet

tcezard · 2025-11-21T12:59:59Z

convert_gvf_to_vcf/convertGVFtoVCF.py

+def merge_vcf_objects(previous, current, list_of_sample_names):
+    """ Merge VCF objects.
+    :params: previous: previous VCF line object
+    :params: current: current VCF line object
+    :params: list_of_sample_names: sample names
+    :return: merged_object
+    """
+    merged_object = previous.merge(current, list_of_sample_names)
+    return merged_object
+
+def keep_vcf_objects(previous, list_of_sample_names):
+    """ Keep VCF objects.
+    :params: previous VCF line object
+    :return: kept_object
+    """
+    kept_object = previous.keep(list_of_sample_names)
+    return kept_object


These two functions seems unnecessary.

not addressed yet

tcezard · 2025-11-21T13:02:57Z

convert_gvf_to_vcf/vcfline.py

+                )
+
+    def keep(self, list_of_sample_names):
+        self.format_values_by_sample_string = self.combine_format_values_by_sample(self.format_dict, list_of_sample_names)


This should not be assigned to self.

not addressed yet

tcezard · 2025-11-21T13:08:54Z

convert_gvf_to_vcf/vcfline.py

+        return self.info_string
+
+    # MERGE OR KEEP below
+    def merge(self, other_vcf_line, list_of_sample_names):


The merge and keep functions are returning a set of strings ready to be printed where I think you should keep the information in the VcfLine object until the end and print them using the __str__

addressed: return self and formatted with str

tcezard · 2025-11-21T13:10:23Z

convert_gvf_to_vcf/vcfline.py

+                self.format_values_by_sample_string
+                )
+
+    def keep(self, list_of_sample_names):


The keep function does not do much except updating the list of samples in the VCF line. I think you should change the name of the function to describe what it actually does.

not addressed yet

…__str__ to write the vcf line object

khetherin added 6 commits November 10, 2025 15:39

dictionary comparison

09920e4

fixed issue so FORMAT sample values in VCF file are all present

e00bea3

added format to compare_and_merge_lines

9df757b

edited format to compare_and_merge_lines

129f129

tidy

579db86

tidy

120db8a

khetherin closed this Nov 12, 2025

khetherin reopened this Nov 12, 2025

khetherin added 2 commits November 12, 2025 10:10

edited test function name

49984b8

edited test function name

a3e7e3c

khetherin force-pushed the mergelines branch from 2489ce4 to a3e7e3c Compare November 12, 2025 10:12

edited test function

f6cca1f

khetherin requested a review from tcezard November 12, 2025 10:17

deal with nested dictionaries better

02a3ac2

tcezard reviewed Nov 13, 2025

View reviewed changes

khetherin added 3 commits November 14, 2025 16:33

reformatting function format_sample_values

89e6933

tests passed

a1a24b6

khetherin requested a review from tcezard November 20, 2025 17:03

tcezard requested changes Nov 21, 2025

View reviewed changes

khetherin added 10 commits November 24, 2025 12:09

removed redundant code and moved code to setUp

c6f3af3

added comments

b4c3c34

removed empty lines

fa0d021

focused on removing INFO string. Use info_dict to store values. Uses …

0a15978

…__str__ to write the vcf line object

check for presence in dictionary before deletion

c93a092

correct formatting IMPRECISE in INFO

3d0ff68

removed dead code

407c27b

removed dead code

52f7029

removed empty line

e02ee5e

added comments

cb25aab

khetherin added 10 commits November 25, 2025 14:50

removed dead code

7626e99

replaced with f-string

9cd2973

minor edit

423cc68

ordered the format keys and format the FORMAT keys string in __str__

e533c59

minor docstring edit

ac818e7

removed format_values_by_sample_string

6a4a4e0

removed duplicate merged VCF lines. removed extraneous ID in INFO

a21658c

adjusted algorithm for merging

4015852

edited testing

9cc23a2

minor edit

c98c291

khetherin requested a review from tcezard November 28, 2025 12:46

edited test_format_sample_values

a0341e5

tcezard approved these changes Nov 30, 2025

View reviewed changes

tcezard merged commit a358048 into EBIvariation:main Dec 1, 2025
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khetherin commented Nov 10, 2025

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