<reponame>Edinburgh-Genome-Foundry/Primavera<filename>tests/test_primer_selection.py<gh_stars>10-100
import os
import matplotlib

matplotlib.use("Agg")
from primavera import load_record, Primer, PrimerSelector


constructs_path = os.path.join("tests", "data", "constructs")
primers_path = os.path.join("tests", "data", "available_primers.fa")


def test_PrimerSelector(tmpdir):
    records = [
        load_record(os.path.join(constructs_path, f), linear=False)
        for f in sorted(os.listdir(constructs_path))
        if f.endswith(".gb")
    ][:3]
    available_primers = Primer.list_from_fasta(primers_path)

    # SELECT THE BEST PRIMERS
    selector = PrimerSelector(read_range=(150, 800), tm_range=(55, 70))
    selected_primers = selector.select_primers(records, available_primers)

    # WRITE ALL PRIMERS IN A CSV FILE (PRIMERS TO ORDER ARE FIRST)
    csv_path = os.path.join(str(tmpdir), "primer_selection_example.csv")
    table = selector.write_primers_table(
        selected_primers=selected_primers, csv_path=csv_path
    )
    assert table.available.sum() == 2

    selector.write_records_primers_table(
        selected_primers=selected_primers, records=records, csv_path=csv_path
    )

    # PLOT THE PREDICTED SEQUENCING COVERAGE FOR EACH CONSTRUCT
    pdf_path = os.path.join(str(tmpdir), "primer_selection_example.pdf")
    selector.plot_coverage(
        records=records, selected_primers=selected_primers, pdf_path=pdf_path
    )
    selector.write_multifile_report(
        records, selected_primers, target=str(tmpdir)
    )
    selector.write_multifile_report(
        records, selected_primers, target=os.path.join(str(tmpdir), "a.zip")
    )
