def build_dot_bracket(self):
# get all the positions
results = db_session \
.query(Structure, Transcript) \
.filter(
Structure.id==self.structure_id,
Transcript.id==Structure.transcript_id
) \
.all()
# Get position values from Structure entity
positions = results[0][0].get_values()
seq_str = results[0][1].get_sequence_str()
dot_bracket_str = build_dot_bracket(positions)
return {
"sequence": seq_str.replace("T", "U"),
"structure": dot_bracket_str
}
def build_dot_bracket(self):
# get all the positions
results = db_session \
.query(Structure, Transcript) \
.filter(
Structure.id==self.structure_id,
Transcript.id==Structure.transcript_id
) \
.all()
# Get position values from Structure entity
positions = results[0][0].get_values()
seq_str = results[0][1].get_sequence_str()
dot_bracket_str = build_dot_bracket(positions)
return {
"sequence": seq_str.replace("T", "U"),
"structure": dot_bracket_str
}
def generate_txt(self, results):
# first we must extract and display the sequence, using the transcript object. output
# in fasta-like format
transcript = results[0][2]
buf = ">" + self.transcript_id + "\n"
buf += insert_newlines(transcript.get_sequence_str()) + "\n"
for result in results:
structure = result[0]
run = result[1]
transcript = result[2]
positions = structure.get_values()
# generate and add the header text for this structure
buf += (">sid_" + str(structure.id) + "\t" + "ENERGY:" +
str(structure.energy) + " kcal/mol\t" + run.description +
"\n")
# generate and add dot bracket text
buf += insert_newlines(build_dot_bracket(positions)) + "\n"
return buf
def generate_txt(self, results):
# first we must extract and display the sequence, using the transcript object. output
# in fasta-like format
transcript = results[0][2]
buf = ">"+self.transcript_id+"\n"
buf += insert_newlines(transcript.get_sequence_str())+"\n"
for result in results:
structure = result[0]
run = result[1]
transcript = result[2]
positions = structure.get_values()
# generate and add the header text for this structure
buf += (
">sid_"+str(structure.id)+"\t"+
"ENERGY:"+str(structure.energy)+" kcal/mol\t"+
run.description+"\n")
# generate and add dot bracket text
buf += insert_newlines(build_dot_bracket(positions))+"\n"
return buf