def print_calc(gene, param_json):
context = {}
e = Ensembl('', gene)
information = e.ensembl3()
if param_json:
return information
else:
if information != Ensembl.GENE_NOT_FOUND_ERROR and information != Ensembl.FAIL_CONNECTION_ERROR:
information = information['seq']
s1 = Seq(information)
a_percentage, c_percentage, g_percentage, t_percentage = s1.percentages()
context['gene'] = gene
context['a_perc'] = a_percentage
context['c_perc'] = c_percentage
context['g_perc'] = g_percentage
context['t_perc'] = t_percentage
context['length'] = s1.len()
contents = read_template_htm_file('html/info/geneCalc.html').render(context=context)
return contents
else:
context['error_msg'] = information
context['type'] = 'gene'
context['input'] = gene
contents = read_template_htm_file('html/not_found_error.html').render(context=context)
return contents
def info(cs, sequence):
print_colored('INFO', 'red')
s = Seq(sequence)
response = 'Total length: ' + str(Seq.len(s)) + "\n" + str(
Seq.percentages(s)) + '\n'
print(response)
cs.send(response.encode())
def gene_calculations(info_dict):
s = Seq(info_dict['seq'])
percentages = Seq.percentages(s)
context = {
'id': info_dict['id'],
"percentages": percentages,
'length': len(info_dict['seq'])
}
content = read_template_html_file("./html/gene_calculations.html").render(
context=context)
return content
def info(sequence):
s = Seq(sequence)
response = 'Total length: ' + str(Seq.len(s)) + "\r" + str(
Seq.percentages(s)) + '\r'
return response
'green')
endpoint6 = "/geneCalc?gene=FXN"
try:
conn.request("GET", endpoint6 + PARAM) # send the request
except ConnectionRefusedError:
print("ERROR! Cannot connect to the Server")
exit()
calc_response = conn.getresponse()
print(f"Response received!: {calc_response.status} {calc_response.reason}\n")
calc_dict = json.loads(calc_response.read().decode())
gene3 = endpoint6.split('?')[1].split('=')[1].split('&')[0]
gene3_object = Seq(calc_dict['seq'])
a_perc, c_perc, g_perc, t_perc = gene3_object.percentages()
termcolor.cprint('GENE ', 'magenta', end='')
termcolor.cprint(gene3, 'blue')
termcolor.cprint('The total length of the gene is: ', 'magenta', end='')
termcolor.cprint(gene3_object.len(), 'blue')
termcolor.cprint('The percentage of the base "A": ', 'magenta', end='')
termcolor.cprint(str(a_perc) + '%', 'blue')
termcolor.cprint('The percentage of the base "C": ', 'magenta', end='')
termcolor.cprint(str(c_perc) + '%', 'blue')
termcolor.cprint('The percentage of the base "G": ', 'magenta', end='')
termcolor.cprint(str(g_perc) + '%', 'blue')
