def test_export_pep_sqlite(self):
args = protgraph.parse_args(["-epepsqlite", "--pep_hops", "2"] +
self.procs_num + self.example_files)
protgraph.prot_graph(**args)
def test_issue13(self):
args = protgraph.parse_args(
["-n", "1",
os.path.join(self.examples_path, "F1SN05.txt")])
protgraph.prot_graph(**args)
def test_met(self):
args = protgraph.parse_args(["-ft", "IniT_MET"] + self.procs_num +
self.example_files)
protgraph.prot_graph(**args)
def test_digestion_trypsin(self):
args = protgraph.parse_args(["-d", "trypsin"] + self.procs_num +
self.example_files)
protgraph.prot_graph(**args)
def test_none(self):
args = protgraph.parse_args(["-ft", "NoNE"] + self.procs_num +
self.example_files)
protgraph.prot_graph(**args)
def test_isoforms(self):
args = protgraph.parse_args(["-ft", "VAR_SeQ"] + self.procs_num +
self.example_files)
protgraph.prot_graph(**args)
def test_statistics_miscleavages(self):
args = protgraph.parse_args(["-cnpm"] + self.procs_num +
self.example_files)
protgraph.prot_graph(**args)
def test_vm_nterm(self):
args = protgraph.parse_args(["-vm", "ntErm:57.021464"] +
self.procs_num + self.example_files)
protgraph.prot_graph(**args)
def test_replacement(self):
args = protgraph.parse_args(["-raa", "A->b,C,d"] + self.procs_num +
self.example_files)
protgraph.prot_graph(**args)
def test_statistics_possibilites(self):
args = protgraph.parse_args(["-cnp"] + self.procs_num +
self.example_files)
protgraph.prot_graph(**args)
def test_annotate_weights(self):
args = protgraph.parse_args(["-aawe", "-amwe"] + self.procs_num +
self.example_files)
protgraph.prot_graph(**args)
def test_no_merge(self):
args = protgraph.parse_args(["-nm"] + self.procs_num +
self.example_files)
protgraph.prot_graph(**args)
def test_digestion_full(self):
args = protgraph.parse_args(["-d", "full"] + self.procs_num +
self.example_files)
protgraph.prot_graph(**args)
def test_issue41(self):
args = protgraph.parse_args([
"-n", "1", "-epepfasta",
os.path.join(self.examples_path, "P49782.txt")
])
protgraph.prot_graph(**args)
def test_statistics_con(self):
args = protgraph.parse_args(["-cnpcon"] + self.procs_num +
self.example_files)
protgraph.prot_graph(**args)
def test_fm_none(self):
args = protgraph.parse_args(["-ft", "none", "-fm", "c:57.021464"] +
self.procs_num + self.example_files)
protgraph.prot_graph(**args)
def test_minimal(self):
args = protgraph.parse_args([] + self.procs_num + self.example_files)
protgraph.prot_graph(**args)
def test_vm_none_cterm(self):
args = protgraph.parse_args(["-ft", "none", "-vm", "CtERM:57.021464"] +
self.procs_num + self.example_files)
protgraph.prot_graph(**args)
def test_export_pickle(self):
args = protgraph.parse_args(["-epickle"] + self.procs_num +
self.example_files)
protgraph.prot_graph(**args)
def test_all(self):
args = protgraph.parse_args(["-ft", "ALl"] + self.procs_num +
self.example_files)
protgraph.prot_graph(**args)
def test_export_lbpcsr(self):
args = protgraph.parse_args(["-elbpcsr"] + self.procs_num +
self.example_files)
protgraph.prot_graph(**args)
def test_variants(self):
args = protgraph.parse_args(["-ft", "VARIAnT"] + self.procs_num +
self.example_files)
protgraph.prot_graph(**args)
def test_export_pep_trie(self):
args = protgraph.parse_args(
["-epeptrie", "--pep_hops", "5"] + self.procs_num +
[os.path.join(self.examples_path, "Q9QXS1.txt")])
protgraph.prot_graph(**args)
def test_signal(self):
args = protgraph.parse_args(["-ft", "SIGnaL"] + self.procs_num +
self.example_files)
protgraph.prot_graph(**args)
("d", ["-ft", "VARIANT"]),
("e", ["-ft", "MUTAGEN"]),
("f", ["-ft", "CONFLICT"]),
("g", ["-ft", "NONE", "-raa", "B->D,N"]),
("h", ["-ft", "NONE", "-raa", "J->I,L"]),
("i", ["-ft", "NONE", "-raa", "Z->Q,E"])
]
input_files = ["../examples/e_coli.dat"]
statistics = ["-cnp", "-n", "9434", "-no_desc"]
counter = 0
for r in range(0, len(used_features) + 1):
for c in itertools.combinations(used_features, r):
counter += 1
print("\nExecuting Iteration {} out of {}".format(
counter, 2**(len(used_features))))
if len(c) != 0:
configuration = [y for x in c for y in x[1]]
else:
configuration = ["-ft", "NONE"]
if len(c) != 0:
output_file = ["-o", "".join([x[0] for x in c]) + ".csv"]
else:
output_file = ["-o", "none.csv"]
args = protgraph.parse_args(statistics + configuration +
output_file + input_files)
protgraph.prot_graph(**args)