如何使用Python随机提取FASTA序列？

Question

我有以下序列，这些序列是带有序列标头及其核苷酸的fasta格式。如何随机提取序列。例如，我想从总序列中随机选择2个序列。提供的工具可以根据百分比而不是序列数进行提取。谁能帮我？

快餐

>chr1:1310706-1310726
GACGGTTTCCGGTTAGTGGAA
>chr1:901959-901979
GAGGGCTTTCTGGAGAAGGAG
>chr1:983001-983021
GTCCGCTTGCGGGACCTGGGG
>chr1:984333-984353
CTGGAATTCCGGGCGCTGGAG
>chr1:1154147-1154167
GAGATCGTCCGGGACCTGGGT

预期产量

>chr1:1154147-1154167
GAGATCGTCCGGGACCTGGGT
>chr1:901959-901979
GAGGGCTTTCTGGAGAAGGAG

Answer 1

如果您正在使用FASTA文件时使用BioPython，获得n序列使用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))

输出：

[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=[])]

您可以根据需要提取字符串：

 print([(seq.name,str(seq.seq)) for seq in  sample(list(seqs),2)])
 [('chr1:1310706-1310726', 'GACGGTTTCCGGTTAGTGGAA'), ('chr1:983001-983021', 'GTCCGCTTGCGGGACCTGGGG')]

如果行始终成对出现，并且您跳过了顶部的元数据，则可以压缩：

from random import sample

with open("foo.fasta") as f:
    print(sample(list(zip(f, f)), 2))

这会给你成对的元组线：

[('>chr1:983001-983021\n', 'GTCCGCTTGCGGGACCTGGGG\n'), ('>chr1:984333-984353\n', 'CTGGAATTCCGGGCGCTGGAG\n')]

要准备编写这些行：

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))

输出：

>chr1:1310706-1310726
GACGGTTTCCGGTTAGTGGAA
>chr1:983001-983021
GTCCGCTTGCGGGACCTGGGG