I have a fasta file as below:
>seq1
AAAAAAAA
>seq2
TTTTTTTT
>seq3
CCCCCCCC
>seq4
GGGGGGGG
I want to get all combinations of the lines (except the ones that start with > sign)
. The desired output should be:
AAAAAAAA
TTTTTTTT
AAAAAAAA
CCCCCCCC
AAAAAAAA
GGGGGGGG
TTTTTTTT
CCCCCCCC
TTTTTTTT
GGGGGGGG
CCCCCCCC
GGGGGGGG
My piece of code is here but the last step of making combinations is missing:
from Bio import SeqIO
list1=[]
with open('file1.fa', 'r') as file1:
for record1 in SeqIO.parse(file1, 'fasta'):
list1.append(record1.seq)
for i in list1:
print(i)
Thank you
try
from itertools import combinations as com
lst = ['A', 'B', 'C', 'D']
combi = list(com(lst, 2))
for entry in combi:
print(entry[0])
print(entry[1])
print()
output
A
B
A
C
A
D
B
C
B
D
C
D
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