def test_split__three_groups(): msa = {"seq1" : "ACGCAT", "seq2" : "GAGTGA"} expected = {"1" : {"seq1" : "AC", "seq2" : "GT"}, "2" : {"seq1" : "CA", "seq2" : "AG"}, "3" : {"seq1" : "GT", "seq2" : "GA"}} with RequiredCall(_VALIDATION_PATH, args = [msa]): assert_equal(split_msa(msa, "123"), expected) with RequiredCall(_VALIDATION_PATH, args = [msa]): assert_equal(split_msa(msa), expected)
def test_split__partial_group(): msa = {"seq1" : "ACGCA", "seq2" : "GAGTG"} expected = {"1" : {"seq1" : "AC", "seq2" : "GT"}, "2" : {"seq1" : "CA", "seq2" : "AG"}, "3" : {"seq1" : "G", "seq2" : "G"}} with RequiredCall(_VALIDATION_PATH, args = [msa]): assert_equal(split_msa(msa), expected)
def test_split__empty_group(): msa = {"seq1" : "AC", "seq2" : "GA"} expected = {"1" : {"seq1" : "A", "seq2" : "G"}, "2" : {"seq1" : "C", "seq2" : "A"}, "3" : {"seq1" : "", "seq2" : ""}} with RequiredCall(_VALIDATION_PATH, args = [msa]): assert_equal(split_msa(msa), expected)
def test_split__three_groups(): msa = {"seq1": "ACGCAT", "seq2": "GAGTGA"} expected = { "1": { "seq1": "AC", "seq2": "GT" }, "2": { "seq1": "CA", "seq2": "AG" }, "3": { "seq1": "GT", "seq2": "GA" } } with RequiredCall(_VALIDATION_PATH, args=[msa]): assert_equal(split_msa(msa, "123"), expected) with RequiredCall(_VALIDATION_PATH, args=[msa]): assert_equal(split_msa(msa), expected)
def test_split_msa__two_groups(): msa = {"seq1": "ACGCAT", "seq2": "GAGTGA"} expected = { "1": { "seq1": "ACCA", "seq2": "GATG" }, "2": { "seq1": "GT", "seq2": "GA" } } with RequiredCall(_VALIDATION_PATH, args=[msa]): assert_equal(split_msa(msa, "112"), expected)
def test_split__partial_group(): msa = {"seq1": "ACGCA", "seq2": "GAGTG"} expected = { "1": { "seq1": "AC", "seq2": "GT" }, "2": { "seq1": "CA", "seq2": "AG" }, "3": { "seq1": "G", "seq2": "G" } } with RequiredCall(_VALIDATION_PATH, args=[msa]): assert_equal(split_msa(msa), expected)
def test_split__empty_group(): msa = {"seq1": "AC", "seq2": "GA"} expected = { "1": { "seq1": "A", "seq2": "G" }, "2": { "seq1": "C", "seq2": "A" }, "3": { "seq1": "", "seq2": "" } } with RequiredCall(_VALIDATION_PATH, args=[msa]): assert_equal(split_msa(msa), expected)
def _run(self, _config, temp): msas = [] for filename in sorted(self._infiles): split_by = self._infiles[filename].get("partition_by", self._part_by) for (key, msa) in sorted(split_msa(read_msa(filename), split_by).items()): for excluded_group in self._excluded: msa.pop(excluded_group) msas.append(("%s_%s" % (self._infiles[filename]["name"], key), msa)) msa = join_msa(*(msa for (_, msa) in msas)) with open(reroot_path(temp, self._out_prefix + ".phy"), "w") as output: output.write(interleaved_phy(msa, add_flag = self._add_flag)) with open(reroot_path(temp, self._out_prefix + ".partitions"), "w") as output: end = 0 for (name, msa) in msas: length = len(msa.itervalues().next()) output.write("DNA, %s = %i-%i\n" % (name, end + 1, end + length)) end += length
def test_split_msa__no_split_by(): split_msa({"seq1": "ACG", "seq2": "GAT"}, split_by="")
def test_split_msa__empty_msa(): split_msa({})
def test_split_msa__single_group(): msa = {"seq1": "ACGCAT", "seq2": "GAGTGA"} expected = {'1': {"seq1": "ACGCAT", "seq2": "GAGTGA"}} with RequiredCall(_VALIDATION_PATH, args=[msa]): assert_equal(split_msa(msa, "111"), expected)
def test_split_msa__no_split_by(): split_msa({"seq1" : "ACG", "seq2" : "GAT"}, split_by = "")
def test_split_msa__empty_msa(): split_msa({})
def test_split_msa__two_groups(): msa = {"seq1" : "ACGCAT", "seq2" : "GAGTGA"} expected = {"1" : {"seq1" : "ACCA", "seq2" : "GATG"}, "2" : {"seq1" : "GT", "seq2" : "GA"}} with RequiredCall(_VALIDATION_PATH, args = [msa]): assert_equal(split_msa(msa, "112"), expected)
def test_split_msa__single_group(): msa = {"seq1" : "ACGCAT", "seq2" : "GAGTGA"} expected = {'1' : {"seq1" : "ACGCAT", "seq2" : "GAGTGA"}} with RequiredCall(_VALIDATION_PATH, args = [msa]): assert_equal(split_msa(msa, "111"), expected)