test_basics.py

import os
import matplotlib

matplotlib.use("Agg")
from crazydoc import CrazydocParser, CrazydocSketcher, records_to_genbank


example_path = os.path.join("tests", "data", "test_sample.docx")
protein_path = os.path.join("tests", "data", "test_protein_seq.docx")


def test_crazydocparser(tmpdir):
    parser = CrazydocParser(
        ["highlight_color", "bold", "underline", "lower_case", "font_color"]
    )
    biopython_records = parser.parse_doc_file(example_path)
    record_features = [
        [(f.location.start, f.location.end, f.qualifiers) for f in record.features]
        for record in biopython_records
    ]
    assert len(
        [
            start
            for start, end, qual in record_features[0]
            if (start, end, qual.get("lower_case", False)) == (1237, 1253, True)
        ]
    )
    records_to_genbank(biopython_records, path=str(tmpdir))

    sketcher = CrazydocSketcher()
    for record in biopython_records:
        sketch = sketcher.translate_record(record)
        ax, _ = sketch.plot()
        ax.set_title(record.id)
        filepath = os.path.join(str(tmpdir), "%s.png" % record.id)
        ax.figure.savefig(filepath, bbox_inches="tight")

    # PROTEIN SEQUENCES:
    biopython_records = parser.parse_doc_file(protein_path, is_protein=True)
    record_features = [
        [(f.location.start, f.location.end, f.qualifiers) for f in record.features]
        for record in biopython_records
    ]

    # Test for names with "/":
    records_to_genbank(biopython_records, path=str(tmpdir), is_protein=True)
    assert os.path.exists(os.path.join(tmpdir, "Protein sequence 2-a.gp"))
    # Test truncation of LOCUS names to 20 characters in Genbank file:
    with open(os.path.join(tmpdir, "Protein sequence with a long name 1.gp")) as f:
        first_line = f.readline()
    first_line.split()[1] == "Protein_sequence_wit"

    sketcher = CrazydocSketcher()
    for record in biopython_records:
        sketch = sketcher.translate_record(record)
        ax, _ = sketch.plot()
        ax.set_title(record.id)
        filename = record.id.replace("/", "-") + ".png"
        filepath = os.path.join(str(tmpdir), filename)
        ax.figure.savefig(filepath, bbox_inches="tight")