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())
"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('-----| Practice 1, Exercise 10 |------')
bases = ["A", "C", "T", "G"]
list_of_genes = ["U5", "ADA", "FRAT1", "FXN", "RNU6_269P" ]
txt = ".txt"
FOLDER = "../SEQUENCES/"
for e in list_of_genes:
s0 = Seq('')
val = 0
base = ''
s0 = s0.read_fasta(FOLDER+e+txt)
dict1 = s0.count()
for i, t in dict1.items():
while t > val:
val = t
base = i
print("Gene ", e, " : Most frequent base: ", base)
from Seq02 import Seq
print("-----| Practice 1, Exercise 6 |------")
s1 = Seq()
s2 = Seq("ACTGA")
s3 = Seq("Invalid sequence")
print("Sequence 1: (Length : ", s1.len(), ")", s1)
print("Bases:", s1.count())
print("Sequence 2: (Length : ", s2.len(), ")", s2)
print("Bases:", s2.count())
print("Sequence 3: (Length : ", s3.len(), ")", s3)
print("Bases:", s3.count())