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)