如何使用Python随机提取FASTA序列？

如果您正在使用FASTA文件时使用BioPython，获得

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from Bio import SeqIOfrom random import samplewith 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 samplewith open("foo.fasta") as f:    print(sample(list(zip(f, f)), 2))

这会给你成对的元组线：

[('>chr1:983001-983021n', 'GTCCGCTTGCGGGACCTGGGGn'), ('>chr1:984333-984353n', 'CTGGAATTCCGGGCGCTGGAGn')]

要准备编写这些行：

from Bio import SeqIOfrom random import samplewith 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：

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