python - 使用 Biopython Entrez 从 fasta 记录访问序列元素

Question

我有一个 refseq ID 列表 (keys_list)，我用它来使用 BioPython Entrez 下拉序列记录。我只想访问返回的 fasta 记录中的序列，但我不想将记录写入文件才能执行此操作。

我正在尝试以下代码

for key in key_list:
   Entrez.email = "myemailaddress"
   handle = Entrez.efetch(db='nuccore', id=key, rettype='fasta')
   record = SeqIO.parse(handle, "fasta")
   for seq_record in SeqIO.parse(record, "fasta"):
    print seq_record.seq

当我运行这个时，我收到错误:

File "/usr/lib64/python2.6/site-packages/Bio/SeqIO/__init__.py", line 538, in parse
  yield r
File "/usr/lib64/python2.6/contextlib.py", line 34, in __exit__
  self.gen.throw(type, value, traceback)
File "/usr/lib64/python2.6/site-packages/Bio/File.py", line 59, in as_handle
  yield handleish
File "/usr/lib64/python2.6/site-packages/Bio/SeqIO/__init__.py", line 537, in parse
  for r in i:
File "/usr/lib64/python2.6/site-packages/Bio/SeqIO/FastaIO.py", line 37, in FastaIterator
  line = handle.readline()
AttributeError: 'generator' object has no attribute 'readline'

如果我使用handle.read()返回整个记录，我可以获得整个fasta记录，但在这个阶段我只想访问核苷酸序列。

谁能帮我解决这个问题吗？

提前非常感谢。

Answer 1

这就是您所需要的。

而不是:

handle = Entrez.efetch(db='nuccore', id=key, rettype='fasta')

试试这个:

handle = Entrez.efetch(db="nucleotide", id=key, retmode="xml") # retmode as 'xml' , db='nucleotide'
features = Entrez.read(handle)[0]
sequence = features['GBSeq_sequence'] # this is your sequence!

它返回一个字符串，该字符串是您的序列:

'ggctcgcatctctccttcacgcgcccgccgccttacctgaggccgccatccacgccggttgagtcgcgttctgccgcctcccgcctgtggtgcctcctgaactacgtccgccgtctaggtaagtttagagctcaggtcgagaccgggcctttgtccggcgctcccttggagcctacctagactcagccggctctccacgctttgcctgaccctgcttgctcaactctacgtctttgtttcgttttctgttctgcgccgttacagatcgaaagttccacccctttccctttcattcacgactgactgccggcttggcccacggccaagtaccggcaactctgctggctcggagccagcgacagcccattctatagcactctccaggagagaaatttagtacacagttgggggctcgtccgggattcgagcgcccctttattccctaggcaatgggccaaatcttttcccgtagcgctagccctattccgcggccgccccgggggctggccgctcatcactggcttaacttcctccaggcggcatatcgcctagaacccggtccctccagttacgatttccaccagttaaaaaaatttcttaaaatagctttagaaacaccggtctggatctgccccattaactactccctcctagccagcctactcccaaaaggataccccggccgggtgaatgaaattttacacatactcatccaaacccaagcccagatcccgtcccgccccgcgccgccgccgccgtcatcctccacccacgaccccccggattctgacccacaaatcccccctccctatgttgagcctacagccccccaagtccttccagtcatgcacccacatggtgcccctcccaaccaccgcccatggcaaatgaaagacctacaggccattaagcaagaagtctcccaagcggcccctggaagcccccagtttatgcagaccatccggcttgcggtgcagcagtttgaccccactgccaaagacctccaagacctcctgcagtacctttgctcctccctcgtggcttccctccatcaccagcagctagatagccttatatcagaggccgaaactcgaggtattacaggttataaccccttagccggtcccctccgtgtccaagccaacaatccacaacaacaaggattaaggcgagaataccagcaactctggctcgccgccttcgccgccctgccagggagtgccaaagacccttcctgggcctctatcctccaaggcctggaggagccttaccacgccttcgtagaacgcctcaacatagctcttgacaatgggctgccagaaggcacgcccaaagaccccattttacgttccttagcctactctaatgcaaacaaagaatgccaaaaattactacaggcccgagggcacactaatagccctctaggagatatgttgcgggcttgtcaggcctggacccccaaagacaaaaccaaagtgttagttgtccagcctaaaaaaccccccccaaatcagccgtgcttccggtgcgggaaagcaggccactggagtcgggactgcactcagcctcgtcctccccctgggccatgccccctatgtcaagatccaactcactggaagcgagactgcccccgcctaaagcccactatcccagaaccagagccagaggaggatgccctcctattagatctccccgccgacatcccacacccaaaaaactccatagggggggaggtttaacctccccccccacattacagcaagtccttcctaaccaagacccaacatctattctgccagttataccgttagatcccgcccgtcggcccgtaattaaagcccagattgacacccagaccagccacccaaagactatcgaagctctactagatacaggagcagacatgacagtccttccgatagccttgttctcaagtaatactcccctcaaaaacacatccgtgttaggggcagggggccaaacccaagatcactttaagctcacctcccttcctgtgctaatacgcctccctttccggacgacgcctattgttttaacatcttgcctagttgataccaaaaacaactgggccatcataggtcgtgatgccttacaacaatgccaaggcgtcctgtacctccctgaggcaaaaaggccgcctgtaatcttgccaatacaggcgccagctgtccttgggctagaacacctcccaaggccccccgaaatcagccagttccctttaaaccagaacgcctccaggccttgcaacacttggtccggaaggccctggaggcaggccatatcgaaccctacaccgggccaggaaataacccagtattcccagttaaaaaagccaatggaacctggcgattcatccacgacctgcgggccactaactctctaaccatagatctctcatcatcttcccccgggccccctgacttgtccagcctgccaactacactagcccacttacaaactatagaccttaaagacgcctttttccaaatccccctacctaaacagttccagccctactttgctttcactgtcccacagcagtgtaactacggccccggcactagatacgcctggagagtactaccccaagggtttaaaaatagtcccaccctgttcgaaatgcagctggcccatatcctgcagcccattcggcaagccttcccccaatgcactattcttcagtacatggatgacattctcctggcaagcccctcccatgcggacctgcaactactctcagaggccacaatggcttccctaatctcccatgggttgcctgtgtccgaaaacaaaacccagcaaacccctggaacaattaagttcctagggcaaataatttcacctaatcacctcacttatgatgcagtccccaaggtacctatacggtcccgctgggcgctacctgaacttcaagccctacttggcgagattcagtgggtctccaaaggaactcctaccttacgccagccccttcacagtctctactgtgccttacaaaggcatactgatccccgagaccaaatatatttaaatccttctcaagttcaatcattagtgcagctgcggcaggccctgtcacagaactgccgcagtagactagtccaaaccctgcccctcctaggggctattatgctgaccctcactggcaccaccactgtggtgttccagtccaagcagcagtggccacttgtctggctacatgcccccctaccccacactagccagtgcccctgggggcagctacttgcctcagctgtgttattactcgacaaatacaccttgcaatcctatggactactctgccaaaccatacatcataacatctccacccaaaccttcaaccaattcattcaaacatctgaccaccccagtgttcctatcttactccaccacagtcaccgattcaaaaatttaggtgcccagactggagaactttggaacacttttcttaaaacaactgccccattggctcctgtgaaagcccttatgccagtgtttactctttcccctgtgatcataaacaccgccccttgcctgttttcagacggatccacctcccaggcagcctatattctctgggacaagcatatattgtcacaaagatcattcccccttccgccaccgcacaagtcggcccaacgggccgaacttctcggacttttgcatggcctctccagcgcccgttcgtggcgctgtctcaacatatttctagactccaagtatctttatcattaccttcggacccttgccctaggcaccttccaaggcaggtcctctcaggccccctttcaggccctcctgccccgcttactatcgcgtaaggtcgtctatttgcaccacgttcgcagccataccaatctacctgatcccatctccaggctcaacgctctcacagatgccctactaatcacccctgtcctgcagctctctcctgcagacctacacagtttcacccattgcggacagacggccctcacactgcaaggggcaaccacaactgaggcctccaatatcctgcgctcttgccacgcctgccgcaaaaataacccacaacatcagatgcctcaaggacacatccgccgtggcctactccctaaccacatctggcaaggcgacattacccatttcaaatataaaaatacactgtatcgccttcatgtatgggtagacaccttttcaggagccatctcagctacccaaaagagaaaagaaacaagctcagaagctatttcctctttgctccaggccattgcctatctaggcaagcctagctacataaacacagacaatggccctgcctatatttcccaagacttcctcaatatgtgtacctcccttgctattcgccatactacccatgtcccctacaatccaaccagctccggacttgtagaacgctctaatggcattcttaaaaccctattatataagtactttactgacaaacccgacctacctatggataatgctctatccatagccctatggacaatcaaccacctaaatgtattaaccaactgccacaaaacccgatggcagcttcaccactccccccgactccagccgatcccagagacacattccctcagcaataaacaaacccattggtattatttcaagcttcctggtcttaatagccgccagtggaaaggaccacaggaggctcttcaagaagctgccggcgctgctctcatcccggtaagcgctagttctgcccagtggatcccgtggaggctcctcaagcgagctgcatgcccaagacccgtcggaggccccgccgatcccaaagaaaaagaccaccaacaccatgggtaagtttctcgccactttgattttattcttccagttctgccccctcatcctcggtgattacagccccagctgctgtactctcacagttggagtctcctcataccactctaaaccctgcaatcctgcccagccagtttgttcatggaccctcgacctgctggccctt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