def test_feature_extraction_kmer():
infile = utils.get_temp_filename('test.fa')
in_dir = os.path.dirname(infile)
shutil.copyfile(utils.get_test_data('example.mito.fasta.shreded.subset'),
infile)
outfile = infile + '.kmer_vector'
script = scriptpath('feature_extraction_kmer.py')
mmp = os.path.abspath("../scripts/gm_parameters/par_11.modified")
print mmp
tmp = os.path.abspath("./")
print tmp
print in_dir
args = [
"--input", infile, "--outfile", outfile, "--taxid", "12345", "--label",
"taxid"
]
utils.runscript(script, args, in_dir)
assert os.path.exists(outfile), outfile
print outfile
data = [x.strip() for x in open(outfile)]
print len(data)
assert len(data) == 54
assert data[1].startswith("12345\tgi|511782593|ref|NC_021399.1") == True
assert data[0].endswith(
"0.00300180108065\t0.00640384230538\t0.00380228136882") == True
assert data[-1].startswith(
"12345\tgi|511782593|ref|NC_021399.1||pos|304493..309493") == True
assert data[-1].endswith(
"0.00300180108065\t0.00500300180108\t0.00200120072043") == True
utils.cleanup()
def test_feature_extraction_metamark():
infile = utils.get_temp_filename('test.fa')
in_dir = os.path.dirname(infile)
shutil.copyfile(utils.get_test_data('example.mito.fasta.shreded.subset'),
infile)
outfile = infile + '.metamark_vector'
script = scriptpath('feature_extraction_metamark.py')
mmp = os.path.abspath("../scripts/gm_parameters/par_11.modified")
print mmp
tmp = os.path.abspath("./")
print tmp
print in_dir
args = [
"--input", infile, "--outfile", outfile, "--tmp", tmp, "--mmp", mmp,
"--taxid", "12345"
]
utils.runscript(script, args, in_dir)
assert os.path.exists(outfile), outfile
print outfile
data = [x.strip() for x in open(outfile)]
print len(data)
assert len(data) == 30
assert data[1].startswith("12345\tgi|511782593|ref|NC_021399.1") == True
assert data[0].endswith("0.018679\t0.016415\t0.016415") == True
assert data[-1].startswith(
"12345\tgi|511782593|ref|NC_021399.1||pos|295582..300582") == True
assert data[-1].endswith("0.023325\t0.019296\t0.021310") == True
utils.cleanup()
def test_shred_fixed():
infile = utils.get_temp_filename('test.fa')
in_dir = os.path.dirname(infile)
shutil.copyfile(utils.get_test_data('example.mito.fasta'), infile)
outfile = infile + '.shred'
script = scriptpath('shred.py')
args = [
"--input", infile, "--shred", "fixed", "--out", outfile, "--testing"
]
utils.runscript(script, args, in_dir)
assert os.path.exists(outfile), outfile
data = [x.strip() for x in open(outfile)]
assert len(data) == 6715
assert data[0].startswith(">gi|408772811|ref|NC_018815.1") == True
assert data[
1] == "CGAGCTACTCCAAGGCAGTCTAATTTATAGGACCCCCCCCGTCTCTGTGGCAAAAGAGTG"
assert data[84] == "ACATGTTTACTGTAGGAATG"
assert data[85].startswith(
">gi|545906466|ref|NC_022258.1||pos|11965..16965 gi|408772797") == True
assert data[-1] == "GCCCTTTACGTTACCTGGTC"
utils.cleanup()
def test_shred_lognorm():
infile = utils.get_temp_filename('test.fa')
in_dir = os.path.dirname(infile)
shutil.copyfile(utils.get_test_data('example.mito.fasta'), infile)
outfile = infile + '.shred'
script = scriptpath('shred.py')
args = [
"--input", infile, "--shred", "lognorm", "--shape", "1.5", "--scale",
"1000", "--loc", "3000", "--out", outfile, "--testing"
]
utils.runscript(script, args, in_dir)
assert os.path.exists(outfile), outfile
data = [x.strip() for x in open(outfile)]
assert len(data) == 5706
assert data[0].startswith(">gi|545906466|ref|NC_022258.1") == True
assert data[
1] == "AGGAAACCTTATTCAATCCGAAGATACCATGAAAATGGGAAATACGGCAAAAGTAAATTA"
assert data[75] == "GTATTAAAACAAGATTTTTTAACA"
assert data[76].startswith(">gi|545601253|ref|NC_022435.1|") == True
assert data[
-1] == "GGTTACTCTCGTTGCGGTTATTGCTAAAAGCAAGGGATATTCACTCAGCAGAAAG"
utils.cleanup()
def teardown(): utils.cleanup()
def teardown():
utils.cleanup()
