Merge pull request #41 from microBioRust/main

PR for microbiorust-py pytests and __init__.py setup improvements

Author: LCrossman

microbiorust-py/microbiorust/__init__.py

@@ -7,7 +7,7 @@
     from . import microbiorust as _base
 
     #list of submodules importable
-    submodules = ["gbk", "embl", "align", "seqmetrics"]
+    submodules = ["gbk", "embl", "align", "seqmetrics", "blast"]
 
     for sub_name in submodules:
         #get the submodule from the base binary

microbiorust-py/tests/__pycache__/test_mbr.cpython-310-pytest-9.0.2.pyc

@@ -0,0 +1,150 @@
+import pytest
+import os
+import microbiorust
+import textwrap
+from pathlib import Path
+
+# --- FIXTURES: Generating Mock Data ---
+
+@pytest.fixture
+def mock_gbk(tmp_path):
+    """Creates a minimal valid GenBank file."""
+    path = tmp_path / "test.gbk"
+    content = textwrap.dedent("""
+        LOCUS       source_1                 910 bp    DNA     linear   CON 01-NOV-2024
+        DEFINITION  Escherichia coli K-12 substr. MG1655.
+        ACCESSION   source_1
+        VERSION     source_1
+        KEYWORDS    .
+        SOURCE      Escherichia coli K-12 substr. MG1655
+          ORGANISM  Escherichia coli K-12 substr. MG1655
+        FEATURES             Location/Qualifiers
+             source          1..910
+                             /organism="K-12 substr. MG1655"
+                             /mol_type="DNA"
+             gene            complement(1..354)
+                             /locus_tag="b3304"
+             CDS             complement(1..354)
+                             /locus_tag="b3304"
+                             /codon_start=1
+                             /gene="rplR"
+                             /translation="MDKKSARIRRATRARRKLQELGATRLVVHRTPRHIYAQVIAPNGSLVAASTVEKAIAEQLKYTGNKDAAAAVGKAVAERALEKGIKDVSFDRSGFQYHGRVQALDAAREAGLQ"
+                             /product="50S ribosomal subunit protein L18"
+             gene            complement(364..897)
+                             /locus_tag="b3305"
+             CDS             complement(364..897)
+                             /locus_tag="b3305"
+                             /codon_start=1
+                             /gene="rplF"
+                             /translation="MSRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHNTLTFGPRDGYADGWAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLSGFSHPVDHQLPAGITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYADVVRTKEAKK"
+                             /product="50S ribosomal subunit protein L6"
+        ORIGIN
+                1 TTAGAACTGA AGGCCAGCTT CACGGGCAGC ATCTGCCAGT GCCTGGACAC GACCATGATA
+               61 TTGGAACCCG GAACGGTCAA AGGATACATC TTTGATGCCT TTTTCCAGAG CGCGTTCAGC
+              121 GACAGCTTTA CCCACAGCTG CAGCCGCGTC TTTGTTACCG GTGTACTTCA GTTGTTCAGC
+              181 GATAGCTTTT TCTACAGTAG AAGCAGCTAC CAGAACTTCA GAACCGTTCG GTGCAATTAC
+              241 CTGTGCGTAA ATGTGACGCG GGGTACGATG TACCACCAGG CGAGTTGCGC CCAGCTCCTG
+              301 GAGCTTGCGG CGTGCGCGGG TCGCACGACG GATACGAGCA GATTTCTTAT CCATAGTGTT
+              361 ACCTTACTTC TTCTTAGCCT CTTTGGTACG CACGACTTCG TCGGCGTAAC GAACACCCTT
+              421 GCCTTTATAA GGCTCAGGAC GACGGTAGGC GCGCAGATCC GCTGCAACCT GGCCGATCAC
+              481 CTGCTTATCA GCGCCTTTCA GCACGATTTC AGTCTGAGTC GGACATTCAG CAGTGATACC
+              541 CGCAGGCAGC TGATGGTCAA CAGGATGAGA GAAACCCAGA GACAGGTTAA TCACATTGCC
+              601 TTTAACCGCT GCACGGTAAC CTACACCAAC CAGCTGCAGC TTCTTAGTGA AGCCTTCGGT
+              661 AACACCGATA ACCATTGAGT TCAGCAGGGC ACGCGCGGTA CCAGCCTGTG CCCAACCGTC
+              721 TGCGTAACCA TCACGCGGAC CGAAGGTCAG GGTATTATCT GCATGTTTAA CTTCAACAGC
+              781 ATCGTTGAGA GTACGAGTCA GCTCGCCGTT TTTACCTTTG ATCGTAATAA CCTGACCGTT
+              841 GATTTTTACG TCAACGCCGG CAGGAACAAC GACCGGTGCT TTAGCAACAC GAGACA
+        //
+    """)
+    path.write_text(content)
+    return str(path)
+
+@pytest.fixture
+def mock_msa(tmp_path):
+    """Creates a mock FASTA alignment file."""
+    path = tmp_path / "align.fasta"
+    content = (
+        ">Seq1\nATGC--AT\n"
+        ">Seq2\nATGC--TT\n"
+        ">Seq3\nATGCGGTT\n"
+    )
+    path.write_text(content)
+    return str(path)
+
+@pytest.fixture
+def mock_blast_tab(tmp_path):
+    """Creates a mock BLAST tabular file."""
+    path = tmp_path / "results.tab"
+    # qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore
+    content = "seqA\tseqB\t99.0\t100\t1\t0\t1\t100\t1\t100\t1e-10\t200.0\n"
+    path.write_text(content)
+    return str(path)
+
+#tests for parsers (gbk, embl)
+
+def test_gbk_conversions(mock_gbk):
+    #test protein sequence extraction
+    #with open(mock_gbk, 'rb') as f:
+    #    print(f"\n[DEBUG] Raw File Content: {f.read()}")
+    faa = microbiorust.gbk_to_faa(mock_gbk)
+    assert os.path.exists(mock_gbk)
+    assert any("b3304" in line for line in faa)
+    
+    #test count
+    count = microbiorust.gbk_to_faa_count(mock_gbk)
+    assert count == 2
+    
+    #test nucleotide sequence extraction
+    fna = microbiorust.gbk_to_fna(mock_gbk)
+    assert any("ttagaactga" in line.lower() for line in fna)
+
+def test_gbk_to_gff(mock_gbk):
+    #this function writes to {filename}.gff and reads again to check
+    microbiorust.gbk_to_gff(mock_gbk, dna=True)
+    gff_path = f"{mock_gbk}.gff"
+    assert os.path.exists(gff_path)
+    with open(gff_path, "r") as f:
+        assert "source_source_1_1" in f.read()
+
+#tests for multiple sequence alignment 
+
+def test_subset_msa(mock_msa):
+    #subset mock alignment: Rows 0-2 (Seq1 & Seq2), Cols 0-4 (ATGC)
+    subset = microbiorust.subset_msa_alignment(mock_msa, (0, 2), (0, 4))
+    print("subset", subset)
+    assert len(subset) == 2  # 2 headers + 2 sequences
+    assert ">Seq1" in subset[0]
+    assert "ATGC" in subset[1]
+
+def test_purge_gaps(mock_msa, tmp_path):
+    out_path = str(tmp_path / "purged.fasta")
+    #threshold 0.5 should remove the '--' columns in Seq1 and Seq2 and write to file
+    microbiorust.purge_gaps(mock_msa, out_path, 0.5)
+    assert os.path.exists(out_path)
+
+def test_get_consensus(mock_msa):
+    #given 'ATGC' is constant in the mock, it should be in consensus
+    consensus = microbiorust.get_consensus(mock_msa)
+    assert consensus.startswith("ATGC")
+
+#tests for Sequence Metrics
+
+def test_hydrophobicity():
+    seq = "MALWMRLLPLLALLALWGPDPAAAFVN"
+    scores = microbiorust.hydrophobicity(seq, window_size=3)
+    assert len(scores) > 0
+    assert all(isinstance(s, float) for s in scores)
+
+def test_amino_counts():
+    seq = "MATAG"
+    counts = microbiorust.amino_counts(seq)
+    assert counts['M'] == 1
+    assert counts['A'] == 2
+
+#test for Async Tabular Parser
+
+def test_parse_tabular(mock_blast_tab):
+    results = microbiorust.parse_tabular(mock_blast_tab)
+    assert len(results) == 1
+    assert results[0]['qseqid'] == "seqA"
+    assert results[0]['bitscore'] == 200.0