Add tests for append_primers

Author: Donaim

micall/tests/test_append_primers.py

@@ -0,0 +1,165 @@
+
+import pytest
+from pathlib import Path
+from Bio import SeqIO
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+
+
+# Import functions/classes from our module.
+# (Assuming the code is in a module named append_primers_module.py.)
+from micall.utils.append_primers import (
+    append_primers_to_record,
+    entry,
+    parse_arguments,
+    append_primers,
+    UserError,
+    DEFAULT_FORWARD_PRIMER,
+    DEFAULT_REVERSE_PRIMER,
+)
+
+
+def test_append_primers_to_record():
+    original_seq = "ATGCGT"
+    record = SeqRecord(Seq(original_seq), id="test", description="dummy")
+    fwd_primer = "AAA"
+    rev_primer = "TTT"
+    new_record = append_primers_to_record(record, fwd_primer, rev_primer)
+    expected_seq = fwd_primer + original_seq + rev_primer
+    assert str(new_record.seq) == expected_seq
+    assert new_record.id == record.id
+    assert new_record.description == record.description
+
+
+def test_parse_arguments_defaults():
+    # simulate command-line arguments,
+    # note that the first two arguments are input and output files.
+    test_args = [
+        "input.fa",
+        "output.fa",
+    ]
+    args = parse_arguments(test_args)
+    # Check that default primers are set.
+    assert args.input_fasta == Path("input.fa")
+    assert args.output_fasta == Path("output.fa")
+    assert args.forward_primer == DEFAULT_FORWARD_PRIMER
+    assert args.reverse_primer == DEFAULT_REVERSE_PRIMER
+
+
+def test_parse_arguments_custom_primers():
+    test_args = [
+        "in.fa",
+        "out.fa",
+        "--forward-primer", "CUSTOMFWD",
+        "--reverse-primer", "CUSTOMREV"
+    ]
+    args = parse_arguments(test_args)
+    assert args.forward_primer == "CUSTOMFWD"
+    assert args.reverse_primer == "CUSTOMREV"
+
+
+@pytest.fixture
+def temp_fasta_file(tmp_path: Path) -> Path:
+    # Create a temporary FASTA file with two records.
+    fasta_path = tmp_path / "input.fa"
+    records = [
+        SeqRecord(Seq("ATGC"), id="rec1", description="first"),
+        SeqRecord(Seq("GATTACA"), id="rec2", description="second"),
+    ]
+    with fasta_path.open("w") as f:
+        SeqIO.write(records, f, "fasta")
+    return fasta_path
+
+
+def test_append_primers_default(temp_fasta_file: Path, tmp_path: Path):
+    # Use default primers.
+    output_path = tmp_path / "output.fa"
+    append_primers(
+        input=temp_fasta_file,
+        output=output_path,
+        forward_primer=DEFAULT_FORWARD_PRIMER,
+        reverse_primer=DEFAULT_REVERSE_PRIMER,
+    )
+    # Now read back the output.
+    records = list(SeqIO.parse(str(output_path), "fasta"))
+    # Check that the primers were appended.
+    for rec in records:
+        # The record sequence should start with DEFAULT_FORWARD_PRIMER
+        # and end with DEFAULT_REVERSE_PRIMER.
+        seq_str = str(rec.seq)
+        assert seq_str.startswith(DEFAULT_FORWARD_PRIMER)
+        assert seq_str.endswith(DEFAULT_REVERSE_PRIMER)
+        # The middle part should be the original sequence. For instance,
+        # for rec1, the original sequence was "ATGC".
+        # We can extract the original: sequence[len(forward): -len(reverse)]
+        original_seq = seq_str[len(DEFAULT_FORWARD_PRIMER): -len(DEFAULT_REVERSE_PRIMER)]
+        # Check that the original sequence exists in the input file.
+        # Without building a dict from the input file, we can simply check that
+        # the extracted sequence is one of the known ones.
+        assert original_seq in {"ATGC", "GATTACA"}
+
+
+def test_append_primers_default_main(temp_fasta_file: Path,
+                                     tmp_path: Path,
+                                     monkeypatch):
+    # Use default primers.
+    output_path = tmp_path / "output.fa"
+
+    monkeypatch.setattr("sys.argv", ["append_primers.py",
+                                     str(temp_fasta_file),
+                                     str(output_path),
+                                     ])
+
+    with pytest.raises(SystemExit) as exinfo:
+        entry()
+
+    ex: SystemExit = exinfo.value
+    assert ex.code == 0
+
+    # Now read back the output.
+    records = list(SeqIO.parse(str(output_path), "fasta"))
+    # Check that the primers were appended.
+    for rec in records:
+        # The record sequence should start with DEFAULT_FORWARD_PRIMER
+        # and end with DEFAULT_REVERSE_PRIMER.
+        seq_str = str(rec.seq)
+        assert seq_str.startswith(DEFAULT_FORWARD_PRIMER)
+        assert seq_str.endswith(DEFAULT_REVERSE_PRIMER)
+        # The middle part should be the original sequence. For instance,
+        # for rec1, the original sequence was "ATGC".
+        # We can extract the original: sequence[len(forward): -len(reverse)]
+        original_seq = seq_str[len(DEFAULT_FORWARD_PRIMER): -len(DEFAULT_REVERSE_PRIMER)]
+        # Check that the original sequence exists in the input file.
+        # Without building a dict from the input file, we can simply check that
+        # the extracted sequence is one of the known ones.
+        assert original_seq in {"ATGC", "GATTACA"}
+
+
+def test_append_primers_custom(temp_fasta_file: Path, tmp_path: Path):
+    output_path = tmp_path / "output_custom.fa"
+    custom_fwd = "CUSTOMFWD"
+    custom_rev = "CUSTOMREV"
+    append_primers(
+        input=temp_fasta_file,
+        output=output_path,
+        forward_primer=custom_fwd,
+        reverse_primer=custom_rev,
+    )
+    records = list(SeqIO.parse(str(output_path), "fasta"))
+    for rec in records:
+        seq_str = str(rec.seq)
+        assert seq_str.startswith(custom_fwd)
+        assert seq_str.endswith(custom_rev)
+
+
+def test_append_primers_missing_input(tmp_path: Path):
+    # Create a non-existent input file path.
+    missing_file = tmp_path / "non_existent.fa"
+    output_file = tmp_path / "output.fa"
+    with pytest.raises(UserError):
+        append_primers(
+            input=missing_file,
+            output=output_file,
+            forward_primer=DEFAULT_FORWARD_PRIMER,
+            reverse_primer=DEFAULT_REVERSE_PRIMER,
+        )