Source code for croissance.formats.output

import csv

from croissance.estimation import AnnotatedGrowthCurve, GrowthPhase




class TSVWriter:
    def __init__(self, filepath, exclude_default_phase: bool = True):
        self._exclude_default_phase = exclude_default_phase
        self._handle = open(filepath, "wt")
        self._writer = csv.writer(
            self._handle, delimiter="\t", quoting=csv.QUOTE_MINIMAL
        )

        self._writer.writerow(
            ["name", "phase", "start", "end", "slope", "intercept", "N0", "SNR", "rank"]
        )



    def write(self, name: str, curve: AnnotatedGrowthCurve):
        if not self._exclude_default_phase:
            phase = GrowthPhase.pick_best(curve.growth_phases, "rank")
            if phase is None:
                phase = GrowthPhase(None, None, None, None, None, None, None)

            self._write_phase(name, 0, phase)

        for idx, phase in enumerate(curve.growth_phases, start=1):
            self._write_phase(name, idx, phase)


    def _write_phase(self, name, idx, phase):
        self._writer.writerow(
            [
                name,
                idx,
                phase.start,
                phase.end,
                phase.slope,
                phase.intercept,
                phase.n0,
                phase.SNR,
                phase.rank,
            ]
        )

    def __enter__(self):
        return self

    def __exit__(self, *args, **kwargs):
        self.close()



    def close(self):
        self._handle.close()