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Commit 61b0882e authored by Gina's avatar Gina
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fa = open("fasta.fa",'r')
lines = fa.readlines()
for x in range(int(len(lines)/2)):
if x == 0:
annotation = lines[0]
read = lines[1]
if x >= 1:
if lines[2*x] == lines[2*(x-1)]:
read+= lines[(2*x)+1]
else:
annotation = lines[2*x]
read = lines[(2*x)+1]
# Function for random addition of polyA to sequences
import numpy as np
listA = ['A','U','G','C']
''.join(np.random.choice(listA,250,p=[0.9,0.040,0.020,0.020]))
def exon_concatenation:
fa = open("fasta.fa",'r')
lines = fa.readlines()
for x in range(int(len(lines)/2)):
if x == 0:
annotation = lines[0]
read = lines[1]
if x >= 1:
if lines[2*x] == lines[2*(x-1)]:
read+= lines[(2*x)+1]
else:
return annotation
return read
annotation = lines[2*x]
read = lines[(2*x)+1]
import numpy as np
def PolyA_generator(exon):
listA = ['A','T','G','C']
polyA = ''.join(np.random.choice(listA,250,p=[0.9,0.040,0.020,0.020]))
return (exon+polyA)
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