significant restructuring

Author: khetherin

convert_gvf_to_vcf/assistingconverter.py

@@ -0,0 +1,106 @@
+# this is an assistant converter to help convert gvf attributes
+import os
+from convert_gvf_to_vcf.utils import read_info_attributes
+from convert_gvf_to_vcf.helpers import generate_custom_structured_meta_line
+# setting up paths to useful directories
+convert_gvf_to_vcf_folder = os.path.dirname(__file__)
+etc_folder = os.path.join(convert_gvf_to_vcf_folder, 'etc')
+
+def get_gvf_attributes(column9_of_gvf):
+    """Get a dictionary of GVF attributes
+    :param column9_of_gvf:  column - the final column of the GVF file
+    :return: gvf_attribute_dictionary: a dictionary of attribute keys and their values
+    """
+    gvf_attribute_dictionary = {}  # attribute key => value
+    # parse by semicolon this creates attribute
+    # parse by equals sign this creates tag-values, if the value is a comma, create a list
+    attributes_in_gvf_line = column9_of_gvf.split(";")
+    for attribute in attributes_in_gvf_line:
+        attribute_key, attribute_value = attribute.split("=")
+        if "," in attribute_value:
+            attribute_value_list = attribute_value.split(",")
+            gvf_attribute_dictionary[attribute_key] = attribute_value_list
+        else:
+            gvf_attribute_dictionary[attribute_key] = attribute_value
+    return gvf_attribute_dictionary
+
+class Assistingconverter:
+    @staticmethod
+    def convert_gvf_attributes_to_vcf_values(column9_of_gvf,
+                                             info_attribute_dict,
+                                             field_lines_dictionary,
+                                             all_possible_lines_dictionary):
+        gvf_attribute_dictionary = get_gvf_attributes(column9_of_gvf)
+        vcf_vals = {}
+        catching_for_review = []
+        # print("dgva_attribute_dict", dgva_attribute_dict)
+        mapping_attribute_dict = read_info_attributes(os.path.join(etc_folder, 'attribute_mapper.tsv'))
+        # created a rough guide to attributes_for_custom_structured_metainformation in INFOattributes.tsv = this probably should be refined at a later date
+        # TODO: edit INFOattributes.tsv i.e. replace unknown placeholders '.' with the actual answer, provide a more informative description
+        for attrib_key in gvf_attribute_dictionary:
+            # if dgva specific key, create custom INFO tag's meta information line
+            if attrib_key in info_attribute_dict:
+                field_lines_dictionary["INFO"].append(
+                    generate_custom_structured_meta_line(
+                        vcf_key="INFO", vcf_key_id=attrib_key,
+                        vcf_key_number=info_attribute_dict[attrib_key][1],
+                        vcf_key_type=info_attribute_dict[attrib_key][2],
+                        vcf_key_description=info_attribute_dict[attrib_key][3],
+                        optional_extra_fields=None)
+                )
+                vcf_vals[attrib_key] = gvf_attribute_dictionary[attrib_key]
+            elif attrib_key in mapping_attribute_dict:
+                field = mapping_attribute_dict[attrib_key][1]
+                key_for_field = mapping_attribute_dict[attrib_key][2]
+                field_lines_dictionary[field].append(all_possible_lines_dictionary[field][key_for_field])
+
+            elif attrib_key == "sample_name":
+                # sample_names.append(sample_names)
+                pass
+            # GVF keys (not dgva specific)
+            elif attrib_key == "ID":
+                pass
+            elif attrib_key == "Variant_seq":
+                pass
+            elif attrib_key == "Reference_seq":
+                pass
+
+            elif attrib_key == "Dbxref":
+                # custom info tag + pase and add to id?
+                pass
+            elif attrib_key == "Variant_reads":
+                # reserved info/format key, AD/AC
+                pass
+            elif attrib_key == "Zygosity":
+                # format and GT tag
+                pass
+            elif attrib_key == "Phased":
+                # GT or FORMAT PS
+                pass
+            elif attrib_key == "Start_range":
+                # either custom info tag or CIPOS or CIEND, may need imprecise
+                pass
+            elif attrib_key == "End_range":
+                # either custom info tag or CIEND, may need imprecise
+                pass
+            elif attrib_key == "Breakpoint_range":
+                # either custom info tag or CIPOS, CIEND, may need imprecise
+                pass
+            elif attrib_key == "Individual":
+                # sampl name for each column
+                pass
+            # elif attrib_key == "Total_reads":
+            #     # reserved info key, DP
+            #     pass
+            # elif attrib_key == "Variant_freq":
+            #     # reserve info tag, AF
+            #     pass
+            # elif attrib_key == "Genotype":
+            #     # GT
+            #     pass
+            else:
+                print("catching these attribute keys for review at a later date", attrib_key)
+                catching_for_review.append(attrib_key)
+        # print("dictionary", gvf_attribute_dictionary)
+        # print("vcf_vals", vcf_vals)
+        return gvf_attribute_dictionary