def test_sequence_to_eden_id_attribute(self):
"""Test if networkx graph ids are set correctly to fasta header. -> header annotation won't be moved to garden"""
fa_fn = "test/test_fasta_to_sequence_with_center_annotation.fa"
graphs = sequence_to_eden(fasta_to_sequence(fa_fn))
graph = graphs.next()
assert graph.graph["id"] == "ID0 center:25"
def run_rnashape(sequence):
#
cmd = 'echo "%s" | ./RNAshapes -t %d -c %d -# %d' % (sequence,5, 10, 1)
#out = sp.check_output(cmd, shell=True)
#print out
text = []
fp = os.popen(cmd, 'r')
for line in fp:
text.append(line)
fp.close()
#text = out.strip().split('\n')
#out.close()
seq_info = text[0]
if 'configured to print' in text[-1]:
struct_text = text[-2]
else:
struct_text = text[1]
# shape:
structur = struct_text.split()[1]
# extract the shape bracket notation
#shape_list += [line.split()[2] for line in struct_text]
#encoee strucyrte
graph = sequence_to_eden([("ID", sequence)]).next()
graph.graph['structure']=structur
annotate_single(graph)
encode_struct = ''.join([ x["entity_short"].upper() for x in graph.node.values() ])
gc.collect()
return encode_struct
def _serial_graph_motif(self, seqs, placeholder=None):
# make graphs
iterable = sequence_to_eden(seqs)
# use node importance and 'position' attribute to identify max_subarrays of a specific size
graphs = self.vectorizer.annotate(iterable, estimator=self.estimator)
# use compute_max_subarrays to return an iterator over motives
motives = []
for graph in graphs:
subarrays = compute_max_subarrays(graph=graph, min_subarray_size=self.min_subarray_size, max_subarray_size=self.max_subarray_size)
for subarray in subarrays:
motives.append(subarray['subarray_string'])
return motives
def test_symmetric_reweighting_no_annotation(self):
"""This function always expectes annotation of the center position to be
set using format "center:int" in the fasta header."""
graph = sequence_to_eden([("ID", "ACGUACGUAC")])
try:
graph = va.symmetric_trapezoidal_reweighting(graph,
high_weight=1,
low_weight=0,
radius_high=1,
distance_high2low=2)
[x["weight"] for x in graph.next().node.values()]
except AssertionError:
pass
else:
raise Exception('ExpectedException not thrown')
def test_symmetric_reweighting_no_annotation(self):
"""This function always expectes annotation of the center position to be
set using format "center:int" in the fasta header."""
graph = sequence_to_eden([("ID", "ACGUACGUAC")])
try:
graph = va.symmetric_trapezoidal_reweighting(graph,
high_weight=1,
low_weight=0,
radius_high=1,
distance_high2low=2)
[x["weight"] for x in graph.next().node.values()]
except AssertionError:
pass
else:
raise Exception('ExpectedException not thrown')
def pre_processor(seqs, **args):
seqs = seq_to_seq(seqs,
modifier=mark_modifier,
position=0.5,
mark="%")
seqs = seq_to_seq(seqs,
modifier=mark_modifier,
position=0.0,
mark="@")
seqs = seq_to_seq(seqs,
modifier=mark_modifier,
position=1.0,
mark="*")
graphs = sequence_to_eden(seqs)
return graphs
def _serial_graph_motif(self, seqs, placeholder=None):
# make graphs
iterable = sequence_to_eden(seqs)
# use node importance and 'position' attribute to identify max_subarrays of a specific size
graphs = self.vectorizer.annotate(iterable, estimator=self.estimator)
# use compute_max_subarrays to return an iterator over motives
motives = []
for graph in graphs:
subarrays = compute_max_subarrays(
graph=graph,
min_subarray_size=self.min_subarray_size,
max_subarray_size=self.max_subarray_size)
for subarray in subarrays:
motives.append(subarray['subarray_string'])
return motives
def pre_processor(seqs, **args):
seqs = seq_to_seq(seqs, modifier=mark_modifier, position=0.5, mark='%')
seqs = seq_to_seq(seqs, modifier=mark_modifier, position=0.0, mark='@')
seqs = seq_to_seq(seqs, modifier=mark_modifier, position=1.0, mark='*')
graphs = sequence_to_eden(seqs)
return graphs
def test_fasta_to_sequence_graph():
fa_fn = "test/test_fasta_to_sequence.fa"
seq = fasta_to_sequence(fa_fn)
sequence_to_eden(seq)
def pre_process_graph(iterator):
from eden.converter.fasta import sequence_to_eden
graphs = sequence_to_eden(iterator)
return graphs