Exemplos de Seq0 em Python

Exemplo n.º 1

Arquivo: Ex8.py Projeto: mburgosc2/marina-burgos-practices

import P0.Seq0 as Seq0

gene_folder = "./sequences/"

gene_list = ["U5", "ADA", "FRAT1", "FXN"]

print("------|EXERCISE 8|------")
for gene in gene_list:
    seq = Seq0.seq_read_fasta(gene_folder + gene + ".txt")
    bases_count = Seq0.seq_count(seq)
    print("Gene " + gene + ": Most frequent base: " +
          str(Seq0.max_base(bases_count)))

Exemplo n.º 2

import P0.Seq0 as Seq0
GENE_FOLDER = "./Sequences/"

gene_list = ["U5", "ADA", "FRAT1", "FXN"]

print("------| Exercise 5 |------")
for gene in gene_list:
    seq = Seq0.seq_read_fasta(GENE_FOLDER + gene + ".txt")
    print("Gene " + gene + ":", Seq0.seq_count(seq))

Exemplo n.º 3

import P0.Seq0 as Seq0

FOLDER = "./Sequences/"
ID = "U5.txt"

U5_Seq = Seq0.seq_read_fasta(FOLDER + ID)
print("The first 20 bases are:", U5_Seq[0:19])

Exemplo n.º 4

import P0.Seq0 as Seq0
FOLDER = "./sequences/"
id = "U5.txt"
U5_seq = Seq0.seq_read_fasta(FOLDER + id)
print("------|EXERCISE 6|------")
print("Gene U5:")
U5_seq_correct = U5_seq[0:20]
print("Frag: ", U5_seq_correct)
print("Rev:", Seq0.seq_reverse(U5_seq_correct))

Exemplo n.º 5

Arquivo: Ex2.py Projeto: mburgosc2/marina-burgos-practices

import P0.Seq0 as Seq0
FOLDER = "./sequences/"
id = "U5.txt"
U5_seq = Seq0.seq_read_fasta(FOLDER + id)
print("The first 20 bases are: ", U5_seq[0:20])

Exemplo n.º 6

Arquivo: Ex7.py Projeto: mburgosc2/marina-burgos-practices

import P0.Seq0 as Seq0
FOLDER = "./sequences/"
id = "U5.txt"
U5_seq = Seq0.seq_read_fasta(FOLDER + id)
print("------|EXERCISE 7|------")
print("Gene U5:")
U5_seq_correct = U5_seq[0:20]
print("Frag: ", U5_seq_correct)
print("Rev:", Seq0.seq_complement(U5_seq_correct))

Exemplo n.º 7

import P0.Seq0 as Seq0
gene_folder = "./Sequences/"
gene_list = ["U5", "ADA", "PRAT1", "FXN"]

print("-----| Exercise 3 |------")
for gene in gene_list:
    sequence = Seq0.seq_read_fasta(gene_folder + gene + ".txt")
    print("Gene " + gene + "---------> Length:" + str(Seq0.seq_len(sequence)))

Exemplo n.º 8

Arquivo: ex1.py Projeto: elenamancha02/2020-2021-practices

import P0.Seq0 as seq0

print("We are testing Seq0 module")
seq0.seq_ping()

Exemplo n.º 9

import P0.Seq0 as Seq0

FOLDER = "./Sequences/"
ID = "U5.txt"

U5_Seq = Seq0.seq_read_fasta(FOLDER + ID)
print("------| Exercise 7 |------\nGene U5:\nFrag:", U5_Seq[0:19], "\nComp:",
      Seq0.seq_complement(U5_Seq[0:19]))

Exemplo n.º 10

import P0.Seq0 as Seq0

GENE_FOLDER = "./Sequences/"

gene_list = ["U5", "ADA", "FRAT1", "FXN"]

print("------| Exercise 3 |------")
for gene in gene_list:
    seq = Seq0.seq_read_fasta(GENE_FOLDER + gene + ".txt")
    print("Gene " + gene + " ---> ", Seq0.seq_len(seq))

Exemplo n.º 11

import P0.Seq0 as Seq0

gene_folder = "./Sequences/"
gene_list = ["U5", "ADA", "PRAT1", "FXN"]

print("-----| Exercise 5 |------")
for gene in gene_list:
    sequence = Seq0.seq_read_fasta(gene_folder + gene + ".txt")
    print("Gene ", gene, ":", Seq0.seq_count(sequence))

Exemplo n.º 12

Arquivo: Ex5.py Projeto: mburgosc2/marina-burgos-practices

import P0.Seq0 as Seq0

gene_folder = "./sequences/"

gene_list = ["U5", "ADA", "FRAT1", "FXN"]

print("------|EXERCISE 5|------")
for gene in gene_list:
    seq = Seq0.seq_read_fasta(gene_folder + gene + ".txt")
    print("Gene " + gene + ": " + str(Seq0.seq_count(seq)))

Exemplo n.º 13

import P0.Seq0 as Seq0

gene_folder = "./Sequences/"
gene_list = ["U5", "ADA", "PRAT1", "FXN"]
b = ["A", "C", "T", "G"]
l = []
print("-----| Exercise 8 |------")
for gene in gene_list:
    sequence = Seq0.seq_read_fasta(gene_folder + gene + ".txt")
    print("Gene " + gene)
    for base in b:
        bases = Seq0.seq_count_base(sequence, base)
        l.append(bases)
        print(base + ":", bases)

Exemplo n.º 14

Arquivo: Ex6.py Projeto: ClaireOnline/PNE_2021_Practices

import P0.Seq0 as Seq0

FOLDER = "./Sequences/"
ID = "U5.txt"

U5_Seq = Seq0.seq_read_fasta(FOLDER + ID)
print("------| Exercise 6 |------\nGene U5:\nFrag:", U5_Seq[0:19], "\nRev:",
      Seq0.seq_reverse(U5_Seq[0:19]))

Exemplo n.º 15

import P0.Seq0 as Seq0

GENE_FOLDER = "./Sequences/"

gene_list = ["U5", "ADA", "FRAT1", "FXN"]
base_list = ["A", "C", "T", "G"]

print("------| Exercise 4 |------")
for gene in gene_list:
    seq = Seq0.seq_read_fasta(GENE_FOLDER + gene + ".txt")
    print("\nGene " + gene)
    for base in base_list:
        print(base + ":", Seq0.seq_count_base(seq, base))

Exemplo n.º 16

import P0.Seq0 as Seq0
FOLDER = "./Sequences/U5.txt"
U5_Seq = Seq0.seq_read_fasta(FOLDER)

print("-----| Exercise 6 |------")
print("Gene U5:")
print("Frag:" + U5_Seq[0:20])
print("Rev:" + str(Seq0.seq_reverse(U5_Seq[0:20])))

Exemplo n.º 17

Arquivo: Ex1.py Projeto: mburgosc2/marina-burgos-practices

import P0.Seq0 as Seq0
print("We are testing Seq0 module")
Seq0.seq_ping()

Exemplo n.º 18

import P0.Seq0 as Seq0
gene_folder = "./sequences/"

gene_list = ["U5", "ADA", "FRAT1", "FXN"]
base_list = ["A", "C", "T", "G"]

print("------|EXERCISE 4|------")
for gene in gene_list:
    seq = Seq0.seq_read_fasta(gene_folder + gene + ".txt")
    print("Gene", gene)
    for base in base_list:
        print(base + ": " + str(Seq0.seq_count_base(seq, base)))

Exemplo n.º 19

import P0.Seq0 as Seq0  # o tambien si marcamos P0 como sources root, import Seq 0
"""Implement the seq_read_fasta(filename) function, que tiene que leer y almacenar y devolver el body de un archivo FASTA. 
The head is removed, as well as the '\n' characters. This function should be written in the  Seq0.py file. 

Write a python program for opening the U5.txt file and writing into the console the first 20 bases of the sequence"""

FOLDER = './sequences/'  #Un solo punto significa dentro de la carpeta en el que tenemos este archivo, dos puntos significan dentro de PNE PRACTICES (la carpeta padre del anterior), y asi...
ID = 'ADA.txt'

U5_Seq = Seq0.seq_read_fasta(
    FOLDER + ID
)  #Quita la primera línea de código, almacena el body de un fasta y lo devuelve.
print('The first 20 bases are: ', U5_Seq[0:20])

Exemplo n.º 20

import P0.Seq0 as Seq0
gene_folder = "./Sequences/"
U5 = "U5"
ADA = "ADA"
PRAT1 = "PRAT1"
FXN = "FXN"
base = ["A", "C", "G", "T"]

sequence_U5 = Seq0.seq_read_fasta(gene_folder + U5 + ".txt")
bases = Seq0.seq_count(sequence_U5)
l_U5 = []
for a in bases:
    l_U5.append(bases[a])
    U5_h = l_U5.index(max(l_U5))

sequence_ADA = Seq0.seq_read_fasta(gene_folder + ADA + ".txt")
bases2 = Seq0.seq_count(sequence_ADA)
l_ADA = []
for b in bases2:
    l_ADA.append(bases2[b])
    ADA_h = l_ADA.index(max(l_ADA))

sequence_PRAT1 = Seq0.seq_read_fasta(gene_folder + PRAT1 + ".txt")
bases3 = Seq0.seq_count(sequence_U5)
l_PRAT1 = []
for c in bases3:
    l_PRAT1.append(bases3[c])
    PRAT1_h = l_PRAT1.index(max(l_PRAT1))

sequence_FXN = Seq0.seq_read_fasta(gene_folder + FXN + ".txt")
bases4 = Seq0.seq_count(sequence_FXN)

Exemplo n.º 21

Arquivo: ex7.py Projeto: lagaron/2020-2021-PNE-Practices

import P0.Seq0 as Seq0
FOLDER = "./Sequences/U5.txt"
U5_Seq = Seq0.seq_read_fasta(FOLDER)

print("-----| Exercise 7 |------")
print("Gene U5:")
print ("Frag:" + U5_Seq[0: 20])
print ("Comp:" + str(Seq0.seq_complement(U5_Seq[0: 20])))

Exemplo n.º 22

import P0.Seq0 as Seq0


GENE_FOLDER = "./Sequences/"

gene_list = ["U5", "ADA", "FRAT1", "FXN"]
base_list = ["A", "C", "T", "G"]

print("------| Exercise 8 |------")
for gene in gene_list:
    seq = Seq0.seq_read_fasta(GENE_FOLDER + gene + ".txt")
    sort_freq = sorted(Seq0.seq_count(seq).items(), key=lambda item: item[1], reverse=True)
    print("Gene " + gene + " most frequent base:", sort_freq[0][0])