如何使用Python随机提取FASTA序列? [英] How to randomly extract FASTA sequences using Python?

问题描述

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.谁能帮我吗?

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

预期产量

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

推荐答案

如果您正在使用fasta文件，请使用 BioPython ，要获取n序列，请使用 random.sample :

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))

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=[])]

如果需要，您可以提取字符串:

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')]

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:

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))

哪个会给您成对的元组行:

Which will give you pairs of lines in tuples:

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

要准备好编写以下行:

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

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