def test_write_contig_refs(tmpdir, hcv_db):
contigs_fasta = Path(tmpdir) / "contigs.fasta"
contigs_fasta.write_text("""\
>foo
TCACCAGGACAGCGGGTTGAATTCCTCGTGCAAGCGTGGAA
>bar
CATCACATAGGAGACAGGGCTCCAGGACTGCACCATGCTCGTGTGTGGCGACGAC
""")
contigs_csv = StringIO()
expected_contigs_csv = """\
ref,match,group_ref,contig
HCV-1a,1.0,HCV-1a,TCACCAGGACAGCGGGTTGAATTCCTCGTGCAAGCGTGGAA
HCV-1a,0.75,HCV-1a,CATCACATAGGAGACAGGGCTCCAGGACTGCACCATGCTCGTGTGTGGCGACGAC
"""
blast_csv = StringIO()
expected_blast_csv = """\
contig_num,ref_name,score,match,pident,start,end,ref_start,ref_end
2,HCV-1g,37,0.67,100,19,55,8506,8542
2,HCV-1a,41,0.75,100,15,55,8518,8558
1,HCV-1a,41,1.0,100,1,41,8187,8227
"""
write_contig_refs(str(contigs_fasta), contigs_csv, blast_csv=blast_csv)
assert expected_contigs_csv == contigs_csv.getvalue()
assert expected_blast_csv == blast_csv.getvalue()
def test_write_contig_refs_none(tmpdir, hcv_db):
contigs_fasta = Path(tmpdir) / 'contigs.fasta'
assert not contigs_fasta.exists()
contigs_csv = StringIO()
expected_contigs_csv = """\
ref,match,group_ref,contig
"""
write_contig_refs(str(contigs_fasta), contigs_csv)
assert expected_contigs_csv == contigs_csv.getvalue()
def test_write_contig_refs_not_found(tmpdir, hcv_db):
contigs_fasta = Path(tmpdir) / "contigs.fasta"
contigs_fasta.write_text("""\
>foo
CATCACATAGGAGA
""")
contigs_csv = StringIO()
expected_contigs_csv = """\
ref,match,group_ref,contig
unknown,0,,CATCACATAGGAGA
"""
write_contig_refs(str(contigs_fasta), contigs_csv)
assert expected_contigs_csv == contigs_csv.getvalue()
def test_write_contig_refs_partial_match(tmpdir, hcv_db):
contigs_fasta = Path(tmpdir) / "contigs.fasta"
contigs_fasta.write_text("""\
>foo
TCACCAGGACAGCGGGTTGAATTCCTCGTGCAAGCGTGGAA
>bar
CATCACATAGGAGACAGGGCTCCAGGACTGCACCATGCTCGTGTGTGGCGACGAC
""")
contigs_csv = StringIO()
expected_contigs_csv = """\
ref,match,group_ref,contig
HCV-1a,1.0,HCV-1a,TCACCAGGACAGCGGGTTGAATTCCTCGTGCAAGCGTGGAA
HCV-1a,0.75,HCV-1a,CATCACATAGGAGACAGGGCTCCAGGACTGCACCATGCTCGTGTGTGGCGACGAC
"""
write_contig_refs(str(contigs_fasta), contigs_csv)
assert expected_contigs_csv == contigs_csv.getvalue()
def test_write_contig_refs_reversed_match(tmpdir, hcv_db):
""" If BLAST match is reversed, then reverse the contig before reporting. """
contigs_fasta = Path(tmpdir) / "contigs.fasta"
contigs_fasta.write_text("""\
>foo
TCACCAGGACAGCGGGTTGAATTCCTCGTGCAAGCGTGGAA
>bar
GTCGTCGCCACACACGAGCATGGTGCAGTCCTGGAGCCCTGTCTCCTATGTGATG
""")
contigs_csv = StringIO()
expected_contigs_csv = """\
ref,match,group_ref,contig
HCV-1a,1.0,HCV-1a,TCACCAGGACAGCGGGTTGAATTCCTCGTGCAAGCGTGGAA
HCV-1a,0.75,HCV-1a,CATCACATAGGAGACAGGGCTCCAGGACTGCACCATGCTCGTGTGTGGCGACGAC
"""
write_contig_refs(str(contigs_fasta), contigs_csv)
assert expected_contigs_csv == contigs_csv.getvalue()
def test_write_contig_refs_two_groups(tmpdir, hcv_db):
contigs_fasta = Path(tmpdir) / "contigs.fasta"
contigs_fasta.write_text("""\
>foo
ACCCGCCCCTAATAGGGGCGACACTCCGCCATGAATC
>bar
ACCATGGATCACTCCCCTGTGAGGAACTACTGTCTT
>baz
TGCAATGACAGCTTACAGACGGGTTTCCTCGCTTCCTTGTTTTACACCCA
""")
contigs_csv = StringIO()
expected_contigs_csv = """\
ref,match,group_ref,contig
HCV-2a,1.0,HCV-2b,ACCCGCCCCTAATAGGGGCGACACTCCGCCATGAATC
HCV-1g,1.0,HCV-1g,ACCATGGATCACTCCCCTGTGAGGAACTACTGTCTT
HCV-2b,1.0,HCV-2b,TGCAATGACAGCTTACAGACGGGTTTCCTCGCTTCCTTGTTTTACACCCA
"""
write_contig_refs(str(contigs_fasta), contigs_csv)
assert expected_contigs_csv == contigs_csv.getvalue()
def test_merged_contig(tmpdir, hcv_db):
contigs_fasta = Path(tmpdir) / 'contigs.fasta'
assert not contigs_fasta.exists()
merged_contigs_path = Path(tmpdir) / 'merged_contigs.csv'
merged_contigs_path.write_text("""\
contig
TGCACAAGACCCAACAACAATACAAGAAAAAGTATAAGGATAGGACCAGGA
""")
contigs_csv = StringIO()
expected_contigs_csv = """\
ref,match,group_ref,contig
HIV1-C-BR-JX140663-seed,1.0,HIV1-C-BR-JX140663-seed,TGCACAAGACCCAACAACAATACAAGAAAAAGTATAAGGATAGGACCAGGA
"""
with merged_contigs_path.open() as merged_contigs_csv:
write_contig_refs(str(contigs_fasta),
contigs_csv,
merged_contigs_csv=merged_contigs_csv)
assert expected_contigs_csv == contigs_csv.getvalue()