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()