def struct_graph():
app.logger.info(request.json)
if not request.json:
abort(400, "Missing a json in the request")
if 'seq' not in request.json and 'struct' not in request.json:
abort(400, "Missing seq and struct in the json file")
if re.match("^[ACGTUWSMKRYBDHV]+$", request.json['seq']) is None:
abort(400, "Invalid sequence: {}".format(request.json['seq']))
if re.match("^[\(\)\.\[\]\{\}]+[\*]?$",
request.json['struct']) is None:
abort(400, "Invalid structure: {}".format(request.json['struct']))
if request.json['struct'][-1] == '*':
circular = True
structure = request.json['struct'].strip('*')
else:
circular = False
structure = request.json['struct']
fasta_text = ">{}\n{}\n{}".format(request.json['header'],
request.json['seq'], structure)
try:
result = forna.fasta_to_json(fasta_text, circular)
except Exception as ex:
app.logger.exception(ex)
abort(400, "Secondary structure parsing error: {}".format(str(ex)))
return json.dumps(result), 201
def test_with_pseudoknot1(self):
pk_fasta = """>4QK8_A
GUUGCCGAAUCCGAAAGGUACGGAGGAACCGCUUUUUGGGGUUAAUCUGCAGUGAAGCUGCAGUAGGGAUACCUUCUGUCCCGCACCCGACAGCUAACUCCGGAGGCAAUAAAGGAAGGA
..((((....((....))..(((((....(.....(.[((((....((((((.....))))))..(((((.{{{{{{)))))..)))).)].)....)))))..)))).....}}}}}}.
"""
struct = forna.fasta_to_json(pk_fasta)
self.assertTrue(struct is not None)
def test_with_pseudoknot1(self):
pk_fasta = """>4QK8_A
GUUGCCGAAUCCGAAAGGUACGGAGGAACCGCUUUUUGGGGUUAAUCUGCAGUGAAGCUGCAGUAGGGAUACCUUCUGUCCCGCACCCGACAGCUAACUCCGGAGGCAAUAAAGGAAGGA
..((((....((....))..(((((....(.....(.[((((....((((((.....))))))..(((((.{{{{{{)))))..)))).)].)....)))))..)))).....}}}}}}.
"""
struct = forna.fasta_to_json(pk_fasta)
self.assertTrue(struct is not None)
def test_add_colors_to_graph(self):
struct = forna.fasta_to_json(self.fasta)
colors = {'hi': {3: 'black'}}
struct = forna.add_colors_to_graph(struct, colors)
self.assertEqual(struct['nodes'][2]['color'], 'black')
def test_add_colors_to_graph(self):
struct = forna.fasta_to_json(self.fasta)
colors = {'hi': {3: 'black'}}
struct = forna.add_colors_to_graph(struct, colors)
self.assertEqual(struct['nodes'][2]['color'], 'black')
def test_with_pseudoknot2(self):
pk_fasta = """>4FAW_A
UGUGCCCGGCAUGGGUGCAGUCUAUAGGGUGAGAGUCCCGAACUGUGAAGGCAGAAGUAACAGUUAGCCUAACGCAAGGGUGUCCGUGGCGACAUGGAAUCUGAAGGAAGCGGACGGCAAACCUUCGGUCUGAGGAACACGAACUUCAUAUGAGGCUAGGUAUCAAUGGAUGAGUUUGCAUAACAAAACAAAGUCCUUUCUGCCAAAGUUGGUACAGAGUAAAUGAAGCAGAUUGAUGAAGGGAAAGACUGCAUUCUUACCCGGGGAGGUCUGGAAACAGAAGUCAGCAGAAGUCAUAGUACCCUGUUCGCAGGGGAAGGACGGAACAAGUAUGGCGUUCGCGCCUAAGCUUGAACCGCCGUAUACCGAACGGUACGUACGGUGGUGUGG
.((.[[[[[[..{{{{{{{{{{{...(((.......)))..(((((...{{{{{{{...))))){.{{{...{{{..((((.((((((....))))))))))...)]..}}}...}}}.}.(((((((((((.(.....)...(((((.....([[[..[.[..[[[[[[[..[[[[.)......]]]]...]]]].}}}}}}}...]]]..].]..]]]...))))))))))...))))))...}}}}}}}}}}}...)]]]]](...((((....))))...).......(((.(....(((........)))...))))....(((((..(((.(..).)))...))))).(((((((((((((....)))..))))))))))...."""
struct = forna.fasta_to_json(pk_fasta)
def test_fasta_to_json(self):
fasta = self.fasta
struct = forna.fasta_to_json(fasta)
self.assertTrue('nodes' in struct)
self.assertTrue('links' in struct)
def test_with_pseudoknot2(self):
pk_fasta = """>4FAW_A
UGUGCCCGGCAUGGGUGCAGUCUAUAGGGUGAGAGUCCCGAACUGUGAAGGCAGAAGUAACAGUUAGCCUAACGCAAGGGUGUCCGUGGCGACAUGGAAUCUGAAGGAAGCGGACGGCAAACCUUCGGUCUGAGGAACACGAACUUCAUAUGAGGCUAGGUAUCAAUGGAUGAGUUUGCAUAACAAAACAAAGUCCUUUCUGCCAAAGUUGGUACAGAGUAAAUGAAGCAGAUUGAUGAAGGGAAAGACUGCAUUCUUACCCGGGGAGGUCUGGAAACAGAAGUCAGCAGAAGUCAUAGUACCCUGUUCGCAGGGGAAGGACGGAACAAGUAUGGCGUUCGCGCCUAAGCUUGAACCGCCGUAUACCGAACGGUACGUACGGUGGUGUGG
.((.[[[[[[..{{{{{{{{{{{...(((.......)))..(((((...{{{{{{{...))))){.{{{...{{{..((((.((((((....))))))))))...)]..}}}...}}}.}.(((((((((((.(.....)...(((((.....([[[..[.[..[[[[[[[..[[[[.)......]]]]...]]]].}}}}}}}...]]]..].]..]]]...))))))))))...))))))...}}}}}}}}}}}...)]]]]](...((((....))))...).......(((.(....(((........)))...))))....(((((..(((.(..).)))...))))).(((((((((((((....)))..))))))))))...."""
struct = forna.fasta_to_json(pk_fasta)
def test_fasta_to_json(self):
fasta = self.fasta
struct = forna.fasta_to_json(fasta)
self.assertTrue('nodes' in struct)
self.assertTrue('links' in struct)
def test_fasta_to_json1(self):
fasta = '>hi\nACCGGGUUU\n(.(...).)'
struct = forna.fasta_to_json(fasta)