def test_get_outdir_prodigal_cut():
"""
When using prodigal, and cut at each stretch of 4 'N', check that the output
dir where modified sequence must be store is as expected (in tmp_dir, and adding "-split4N").
"""
soft = "prodigal"
genome = "genome1.fasta"
cut = True
pat = "NNNN+"
gpath, grespath = gfunc.get_output_dir(soft, GEN_PATH, GENEPATH, genome,
cut, pat)
assert gpath == os.path.join(GEN_PATH, "genome1.fasta")
assert grespath == os.path.join(GENEPATH,
"genome1.fasta_prodigal-split4N.fna")
def test_get_outdir_prokka_nocut():
"""
When using prokka, and don't cut sequence, check that the output
dir where modified sequence must be store is as expected (in tmp dir, indicating
"shorter_contigs" because we need to shorten the contig headers for prokka)
"""
soft = "prokka"
genome = "genome1.fasta"
cut = False
pat = None
gpath, grespath = gfunc.get_output_dir(soft, GEN_PATH, GENEPATH, genome,
cut, pat)
assert gpath == os.path.join(GEN_PATH, "genome1.fasta")
assert not grespath
def test_get_outdir_prodigal_nocut():
"""
When we use prodigal, and do not cut at each stretch of 5N, no need to create a modified
sequence. So, check that get_output_dir returns an empty res_path (as we will not create
any new sequence)
"""
soft = "prodigal"
genome = "genome1.fasta"
cut = False
pat = None
gpath, grespath = gfunc.get_output_dir(soft, GEN_PATH, GENEPATH, genome,
cut, pat)
assert not grespath
assert gpath == os.path.join(GEN_PATH, "genome1.fasta")
def test_get_outdir_no_input_seq():
"""
Test that when the given genome name does not exist in the dbpath, it exists in tmp path.
It means that it is a concatenation of 2 files of dbpath, which was saved in tmppath
"""
soft = "prodigal"
genome = "prokka_out_for_test-supHeader.faa"
tmp_path = os.path.join("test", "data", "annotate", "test_files")
cut = True
pat = "NNNNNNN+"
gpath, grespath = gfunc.get_output_dir(soft, GEN_PATH, tmp_path, genome,
cut, pat)
assert gpath == os.path.join(tmp_path, "prokka_out_for_test-supHeader.faa")
assert grespath == os.path.join(
tmp_path, "prokka_out_for_test-supHeader.faa_prodigal-split7N.fna")
def test_get_outdir_prokka_cut():
"""
When using prokka, and cut at each stretch of 3 'N', check that the output
dir where modified sequence must be store is as expected (in tmp_di, indicating "-split3N"
because sequence will be cut)
"""
soft = "prokka"
genome = "genome1.fasta"
cut = True
pat = "NNN+"
gpath, grespath = gfunc.get_output_dir(soft, GEN_PATH, GENEPATH, genome,
cut, pat)
assert gpath == os.path.join(GEN_PATH, "genome1.fasta")
assert grespath == os.path.join(GENEPATH,
"genome1.fasta_prokka-split3N.fna")