Skip to content

pseudocigar handling #84

Description

@nickjhathaway

Currently, there are two issues with pseudocigar handling in create_representative_microhaplotype_dict()

  1. It currently stores pseudocigar as pseudo_cigar, which is not the proper name in the schema (should be pseudocigar)
  2. pseudocigar should be a class of pseudocigar with values for the pseudocigar itself, but also the reference location that the pseudocigar refers to, as this will change how to interpret the pseudocigar

Attempted to fix by change

            if val := get_if_present(row, pseudocigar_col):
                mhap["pseudo_cigar"] = val

to

            if val := get_if_present(row, pseudocigar_col):
                mhap["pseudocigar"] = val

but this goes agains the schema where this should be a object that looks like

"pseudocigar" : {
    "pseudocigar_seq" : "8M", 
    "ref_loc" : 
	{
		"chrom" : "Pf3D7_01_v3",
		"end" : 145621,
		"genome_id" : 0,
		"start" : 145448,
		"strand" : "+"
	}
}

rather than

"pseudocigar" : "8M" 

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Fields

    No fields configured for issues without a type.

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions