<filename>varg/utils/write_report.py
from sys import stdout

from .compare import Comparison


class ReportWriter:
    def __init__(self, compare_iter, vcf_fields):
        """
        Creates report

        Args:
            compare_iter (iterator): Iterator over comparisons
            vcf_fields (dictionary): Fields in VCF to be compared
        """

        self.compare_iter = compare_iter
        self.aggr_stats = StatsHelper()
        self.vcf_fields = vcf_fields

    def write(self):

        for records in self.compare_iter:
            comp = Comparison(
                records[0],
                records[1],
                vcf_keys=self.vcf_fields,
                sample_idx_map=records[2],
            )
            self._update_aggr_stats(comp)
            yield comp
        self.aggr_stats.compile_stats()

    def _update_aggr_stats(self, comp):

        for key, value in comp.comparison.items():
            self.aggr_stats.push_stats(field_name=key, stats=value[2])


class StatsHelper:
    def __init__(self):
        self.stats = dict()

    def _add_field(self, field_name: str):
        self.stats[field_name] = dict()

    def _get_fields(self):
        return list(self.stats.keys())

    def push_stats(self, field_name: str, stats: dict):
        if field_name not in self._get_fields():
            self._add_field(field_name)
            self.stats[field_name]["comparisons"] = 0
        for key, value in stats.items():
            if key == "status":
                if value not in self.stats[field_name].keys():
                    self.stats[field_name][value] = 1
                else:
                    self.stats[field_name][value] += 1
            elif key == "diff":
                if "acc_diff" not in self.stats[field_name].keys():
                    self.stats[field_name]["acc_diff"] = value
                else:
                    self.stats[field_name]["acc_diff"] += value
        self.stats[field_name]["comparisons"] += 1

    def compile_stats(self):

        for key, value in self.stats.items():
            if value.get("acc_diff") is not None:
                acc_diff = self.stats[key].pop("acc_diff")
                self.stats[key]["mean_diff"] = acc_diff / self.stats[key]["comparisons"]

    def __str__(self):
        stats_str = ""
        for field_name, field_value in self.stats.items():
            stats_str += "\n" + field_name
            for key, value in field_value.items():
                stats_str += "\n\t" + key + ": " + str(value)
        return stats_str

    def __dict__(self):
        return self.stats

<filename>varg/utils/write_report.py
from sys import stdout

from .compare import Comparison


class ReportWriter:
    def __init__(self, compare_iter, vcf_fields):
        """
        Creates report

        Args:
            compare_iter (iterator): Iterator over comparisons
            vcf_fields (dictionary): Fields in VCF to be compared
        """

        self.compare_iter = compare_iter
        self.aggr_stats = StatsHelper()
        self.vcf_fields = vcf_fields

    def write(self):

        for records in self.compare_iter:
            comp = Comparison(
                records[0],
                records[1],
                vcf_keys=self.vcf_fields,
                sample_idx_map=records[2],
            )
            self._update_aggr_stats(comp)
            yield comp
        self.aggr_stats.compile_stats()

    def _update_aggr_stats(self, comp):

        for key, value in comp.comparison.items():
            self.aggr_stats.push_stats(field_name=key, stats=value[2])


class StatsHelper:
    def __init__(self):
        self.stats = dict()

    def _add_field(self, field_name: str):
        self.stats[field_name] = dict()

    def _get_fields(self):
        return list(self.stats.keys())

    def push_stats(self, field_name: str, stats: dict):
        if field_name not in self._get_fields():
            self._add_field(field_name)
            self.stats[field_name]["comparisons"] = 0
        for key, value in stats.items():
            if key == "status":
                if value not in self.stats[field_name].keys():
                    self.stats[field_name][value] = 1
                else:
                    self.stats[field_name][value] += 1
            elif key == "diff":
                if "acc_diff" not in self.stats[field_name].keys():
                    self.stats[field_name]["acc_diff"] = value
                else:
                    self.stats[field_name]["acc_diff"] += value
        self.stats[field_name]["comparisons"] += 1

    def compile_stats(self):

        for key, value in self.stats.items():
            if value.get("acc_diff") is not None:
                acc_diff = self.stats[key].pop("acc_diff")
                self.stats[key]["mean_diff"] = acc_diff / self.stats[key]["comparisons"]

    def __str__(self):
        stats_str = ""
        for field_name, field_value in self.stats.items():
            stats_str += "\n" + field_name
            for key, value in field_value.items():
                stats_str += "\n\t" + key + ": " + str(value)
        return stats_str

    def __dict__(self):
        return self.stats

Creates report          Args:             compare_iter (iterator): Iterator over comparisons             vcf_fields (dictionary): Fields in VCF to be compared