def info(cs, list_sequences, argument):
print_colored("INFO", "green")
seq = Seq(list_sequences[int(argument)])
print(seq)
number_dict = seq.count()
len1 = len(str(seq))
percentage_dict = seq.percentage(seq.count_bases(), len1)
response = "Sequence: " + list_sequences[int(
argument)] + "\nTotal length: " + str(len1) + "\n"
for key in number_dict:
response += (str(key) + ": " + str(number_dict[key]) + " (" +
str(percentage_dict[key], ) + "%)\n")
print(response)
cs.send(response.encode())
def percentageSeq(gene, genes_dict):
SERVER = "rest.ensembl.org"
ENDPOINT = "/sequence/id/"
PARAMS = "?content-type=application/json"
ID = genes_dict[gene]
connection = http.client.HTTPConnection(SERVER)
connection.request("GET", ENDPOINT + ID + PARAMS)
response = connection.getresponse()
print(response.status, response.reason)
answer_decoded = response.read().decode()
dict_response = json.loads(answer_decoded)
sequence = Seq(dict_response["seq"])
lenght = sequence.len()
a, c, g, t = sequence.percentage(sequence.count_bases(), lenght)
context = {"A": a, "C": c, "G": g, "T": t, "gene": gene}
content = su.read_template_html_file("HTML/percentageCalc.html").render(
context=context)
return content
"FGFR3": "ENSG00000068078",
"KDR": "ENSG00000128052",
"ANK2": "ENSG00000145362"
}
SERVER = "rest.ensembl.org"
ENDPOINT = "/sequence/id/"
PARAMETERS = "?content-type=application/json"
connection = http.client.HTTPConnection(SERVER)
try:
for key, ID in genes_dict.items():
connection.request("GET", ENDPOINT + ID + PARAMETERS)
response = connection.getresponse()
if response.status == 200:
response_dict = json.loads(response.read().decode())
#response = json.dumps(response_dict, indent=4, sort_keys=True
sequence = Seq(response_dict["seq"])
s_length = sequence.len()
percentages = sequence.percentage()
most_frequent_base = sequence.frequent_base(sequence.count())
print_colored("Gene: ", key, "yellow")
print_colored("Description: ", response_dict['desc'], "yellow")
print_colored("Total length: ", s_length, "yellow")
for key, value in percentages.items():
print_colored(key, value, "blue")
print_colored("Most frequent base: ", most_frequent_base, "yellow")
except KeyError:
print(
"The gene is not inside our dictionary. Choose one of the following: ",
list(genes_dict.keys()))
}
SERVER = "rest.ensembl.org"
ENDPOINT = "/sequence/id/"
PARAMETERS = "?content-type=application/json"
connection = http.client.HTTPConnection(SERVER)
try:
user_gene = input("Enter the gene you want to analise: ")
ID = genes_dict[user_gene]
connection.request("GET", ENDPOINT + ID + PARAMETERS)
response = connection.getresponse()
if response.status == 200:
response_dict = json.loads(response.read().decode())
#print(json.dumps(response_dict, indent=4, sort_keys=True))
sequence = Seq(response_dict["seq"])
s_length = sequence.len()
a, c, g, t = sequence.percentage(sequence.count_bases(), s_length)
most_frequent_base = sequence.frequent_base(sequence.count())
print_colored("Gene: ", user_gene, "yellow")
print_colored("Total length: ", s_length, "yellow")
print(a)
print(c)
print(t)
print(g)
print(most_frequent_base)
except KeyError:
print("The gene is not inside our dictionary. Choose one of the following: ", list(genes_dict.keys()))
