def test_ncbi_stockholm(
namespace_base,
path_ncbi_stockholm,
path_ncbi_stockholm_targets,
tmp_path,
):
"""ncfp collects correct coding sequences for NCBI/Stockholm input.
This test was added as a check for the fix in issue 31.
"""
# Modify default arguments
infile = path_ncbi_stockholm
outdir = tmp_path / "ncbi_stockholm"
args = modify_namespace(namespace_base,
infname=infile,
outdirname=outdir,
stockholm=True)
# Run ersatz command-line
ncfp.run_main(args)
# Compare output (should be no skipped files)
check_files(
outdir,
path_ncbi_stockholm_targets,
("ncfp_aa.fasta", "ncfp_nt.fasta"),
)
def test_small_stockholm_use_protein_id(
namespace_base,
path_uniprot_stockholm_small,
path_uniprot_stockholm_small_use_proteinid_targets,
tmp_path,
):
"""ncfp collects correct coding sequences for small UniProt/Stockholm input."""
# Modify default arguments
infile = path_uniprot_stockholm_small
outdir = tmp_path / "small_stockholm_use_proteinid"
args = modify_namespace(
namespace_base,
infname=infile,
outdirname=outdir,
stockholm=True,
use_protein_ids=True,
)
# Run ersatz command-line
ncfp.run_main(args)
# Compare output (should be no skipped files)
check_files(
outdir,
path_uniprot_stockholm_small_use_proteinid_targets,
("ncfp_aa.fasta", "ncfp_nt.fasta"),
)
def test_basic_ncbi(namespace_base, path_ncbi, path_ncbi_targets, tmp_path):
"""ncfp collects correct coding sequences for basic NCBI input."""
# Modify default arguments
infile = path_ncbi
outdir = tmp_path / "basic_ncbi"
args = modify_namespace(namespace_base, infname=infile, outdirname=outdir)
# Run ersatz command-line
ncfp.run_main(args)
# Compare output
check_files(outdir, path_ncbi_targets, ("ncfp_aa.fasta", "ncfp_nt.fasta"))
def test_alternative_start(namespace_base, path_altstart,
path_altstart_targets, tmp_path):
"""ncfp collects correct coding sequences for NCBI input with alternative start codon."""
infile = path_altstart
outdir = tmp_path / "alternative_start"
args = modify_namespace(namespace_base,
infname=infile,
outdirname=outdir,
alternative_start_codon=True)
# Run ersatz command-line
ncfp.run_main(args)
# Compare output
check_files(outdir, path_altstart_targets,
("ncfp_aa.fasta", "ncfp_nt.fasta"))
def test_basic_uniprot(namespace_base, path_uniprot, path_uniprot_targets,
tmp_path, mock_basic_uniprot):
"""ncfp collects correct coding sequences for basic UniProt input."""
# Modify default arguments
infile = path_uniprot
outdir = tmp_path / "basic_uniprot"
args = modify_namespace(namespace_base, infname=infile, outdirname=outdir)
# Run ersatz command-line
ncfp.run_main(args)
# Compare output
check_files(
outdir,
path_uniprot_targets,
("ncfp_aa.fasta", "ncfp_nt.fasta", "skipped.fasta"),
)
def test_basic_stockholm(namespace_base, path_stockholm,
path_stockholm_targets, tmp_path):
"""ncfp collects correct coding sequences for basic UniProt/Stockholm input."""
# Modify default arguments
infile = path_stockholm
outdir = tmp_path / "basic_stockholm"
args = modify_namespace(namespace_base,
infname=infile,
outdirname=outdir,
stockholm=True)
# Run ersatz command-line
ncfp.run_main(args)
# Compare output (should be no skipped files)
check_files(
outdir,
path_stockholm_targets,
("ncfp_aa.fasta", "ncfp_nt.fasta"),
)