def lengthSeq(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"])
length = sequence.len()
context = {"length": length, "gene": gene}
content = su.read_template_html_file("HTML/lengthCalc.html").render(
context=context)
return content
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
from Seq02 import Seq
print("-----| Practice 1, Exercise 8 |------")
s1 = Seq('NULL')
s2 = Seq("ACTGA")
s3 = Seq("Invalid sequence")
print("Sequence", 1, ": (Length:", s1.len(), ")", s1)
print(f"Bases: {s1.count()}")
print(f"Rev: {s1.reverse(s1)}")
print(f"Comp: {s1.complement(s1)}")
print("Sequence", 2, ": (Length:", s2.len(), ")", s2)
print(f"Bases: {s2.count()}")
print(f"Rev: {s2.reverse(s2)}")
print(f"Comp: {s2.complement(s2)}")
print("Sequence", 3, ": (Length:", s3.len(), ")", s3)
print(f"Bases: {s3.count()}")
print(f"Rev: {s3.reverse(s3)}")
print(f"Comp: {s3.complement(s3)}")
"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()))
from Seq02 import Seq
print('-----| Exercise 1 |------')
seq_list = Seq('ACTGA')
print('Sequence: 1 , (Lenght : ' + str(seq_list.len()) + " ) " + str(seq_list))
from Seq02 import Seq
print("-----| Practice 1, Exercise 4 |------")
s1 = Seq('NULL')
s2 = Seq("ACTGA")
s3 = Seq("ERROR")
print("Sequence 1: (Length : ", s1.len(), ")", s1)
print("Sequence 1: (Length : ", s2.len(), ")", s2)
print("Sequence 1: (Length : ", s3.len(), ")", s3)
