comparison scripts/outputs.py @ 20:6ab1a261520a draft

planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty

19:2f7702fd0a4c

# They change depending on whether the run was monomer or multimer
PLDDT_KEY = {
    'monomer': 'plddts',
    'multimer': 'iptm+ptm',
}


class Settings:
    """Parse and store settings/config."""
    def __init__(self):

def write_confidence_scores(ranking: ResultRanking, context: ExecutionContext):
    """Write per-model confidence scores."""
    path = context.settings.workdir / OUTPUTS['model_confidence_scores']
    with open(path, 'w') as f:
        for rank in range(1, 6):
            score = ranking.get_plddt_for_rank(rank)
            f.write(f'ranked_{rank - 1}\t{score:.2f}\n')


def write_per_residue_scores(

            plt.ylabel('Aligned residue')

        plt.savefig(png_path)


def main():
    """Parse output files and generate additional output files."""
    settings = Settings()
    context = ExecutionContext(settings)
    ranking = ResultRanking(context)
    write_confidence_scores(ranking, context)
    rekey_relax_metrics(ranking, context)

    # Optional outputs
    if settings.output_model_pkls:
        rename_model_pkls(ranking, context)
    if settings.output_model_plots:

20:6ab1a261520a

# They change depending on whether the run was monomer or multimer
PLDDT_KEY = {
    'monomer': 'plddts',
    'multimer': 'iptm+ptm',
}

HTML_PATH = Path(__file__).parent / "alphafold.html"
HTML_OUTPUT_FILENAME = 'alphafold.html'
HTML_BUTTON_ATTR = 'class="btn" id="btn-ranked_{rank}"'
HTML_BUTTON_ATTR_DISABLED = (
    'class="btn disabled" id="btn-ranked_{rank}" disabled')


class Settings:
    """Parse and store settings/config."""
    def __init__(self):

def write_confidence_scores(ranking: ResultRanking, context: ExecutionContext):
    """Write per-model confidence scores."""
    path = context.settings.workdir / OUTPUTS['model_confidence_scores']
    with open(path, 'w') as f:
        for rank in range(1, len(context.model_pkl_paths) + 1):
            score = ranking.get_plddt_for_rank(rank)
            f.write(f'ranked_{rank - 1}\t{score:.2f}\n')


def write_per_residue_scores(

            plt.ylabel('Aligned residue')

        plt.savefig(png_path)


def template_html(context: ExecutionContext):
    """Template HTML file.

    Remove buttons that are redundant with limited model outputs.
    """
    print("Templating HTML file...")
    with open(HTML_PATH) as f:
        html = f.read()
    for i in range(len(context.model_pkl_paths), 5):
        btn_id = HTML_BUTTON_ATTR.format(rank=i)
        btn_attr_disabled = HTML_BUTTON_ATTR_DISABLED.format(rank=i)
        html = html.replace(btn_id, btn_attr_disabled)
    with open(context.settings.output_dir / HTML_OUTPUT_FILENAME, 'w') as f:
        f.write(html)


def main():
    """Parse output files and generate additional output files."""
    settings = Settings()
    context = ExecutionContext(settings)
    ranking = ResultRanking(context)
    write_confidence_scores(ranking, context)
    rekey_relax_metrics(ranking, context)
    template_html(context)

    # Optional outputs
    if settings.output_model_pkls:
        rename_model_pkls(ranking, context)
    if settings.output_model_plots: