I have the following sequences which is in a fasta format with sequence header and its nucleotides. How can I randomly extract the sequences. For example I would like to randomly select 2 sequences out of the total sequences. There are tools provided to do so is to extract according to percentage but not the number of sequences. Can anyone help me?
A.fasta
>chr1:1310706-1310726
GACGGTTTCCGGTTAGTGGAA
>chr1:901959-901979
GAGGGCTTTCTGGAGAAGGAG
>chr1:983001-983021
GTCCGCTTGCGGGACCTGGGG
>chr1:984333-984353
CTGGAATTCCGGGCGCTGGAG
>chr1:1154147-1154167
GAGATCGTCCGGGACCTGGGT
Expected Output
>chr1:1154147-1154167
GAGATCGTCCGGGACCTGGGT
>chr1:901959-901979
GAGGGCTTTCTGGAGAAGGAG
If you are working with fasta files use BioPython, to get n
sequences use random.sample:
from Bio import SeqIO
from random import sample
with open("foo.fasta") as f:
seqs = SeqIO.parse(f,"fasta")
print(sample(list(seqs), 2))
Output:
[SeqRecord(seq=Seq('GAGATCGTCCGGGACCTGGGT', SingleLetterAlphabet()), id='chr1:1154147-1154167', name='chr1:1154147-1154167', description='chr1:1154147-1154167', dbxrefs=[]), SeqRecord(seq=Seq('GTCCGCTTGCGGGACCTGGGG', SingleLetterAlphabet()), id='chr1:983001-983021', name='chr1:983001-983021', description='chr1:983001-983021', dbxrefs=[])]
You can extract the strings if necessary:
print([(seq.name,str(seq.seq)) for seq in sample(list(seqs),2)])
[('chr1:1310706-1310726', 'GACGGTTTCCGGTTAGTGGAA'), ('chr1:983001-983021', 'GTCCGCTTGCGGGACCTGGGG')]
If the lines were always in pairs and you skipped the metadata at the top you could zip:
from random import sample
with open("foo.fasta") as f:
print(sample(list(zip(f, f)), 2))
Which will give you pairs of lines in tuples:
[('>chr1:983001-983021\n', 'GTCCGCTTGCGGGACCTGGGG\n'), ('>chr1:984333-984353\n', 'CTGGAATTCCGGGCGCTGGAG\n')]
To get the lines ready to be written:
from Bio import SeqIO
from random import sample
with open("foo.fasta") as f:
seqs = SeqIO.parse(f, "fasta")
samps = ((seq.name, seq.seq) for seq in sample(list(seqs),2))
for samp in samps:
print(">{}\n{}".format(*samp))
Output:
>chr1:1310706-1310726
GACGGTTTCCGGTTAGTGGAA
>chr1:983001-983021
GTCCGCTTGCGGGACCTGGGG