Biopython 从整个基因组中检索特定的 CDS

Question

我是 Whosebug 的新手。我正在尝试使用 Biopython 自动执行搜索过程。我有两个列表，一个是蛋白质 GI 编号，另一个是相应的核苷酸 GI 编号。例如：

protein_GI=[588489721,788136950,409084506]

nucleo_GI=[588489708,788136846,409084493]

第二个列表是使用 ELink 创建的。然而，核苷酸 GI 对应于整个基因组。我需要从每个与蛋白质 GI 匹配的基因组中检索特定的 CDS。我尝试再次使用具有不同 link 名称（"protein_nucleotide_cds"、"protein_nuccore"）的 ELink，但我得到的只是整个基因组的 ID 号。我应该试试其他 link 个名字吗？我还尝试了以下 EFetch 代码：

import Bio
from Bio import Entrez
Entrez.email = None

handle=Entrez.efetch(db="sequences",id="588489708,588489721",rettype="fasta",retmode="text")
print(handle.read())

这种方法在fasta文件中给出了核苷酸和蛋白质序列，但核苷酸序列是整个基因组。

如果有人能帮助我，我将不胜感激。提前致谢！

Answer 1

希望对你有帮助

import Bio
from Bio import Entrez
from Bio import SeqIO
Entrez.email = "mail@example.com"

gi_protein = "GI:588489721"
gi_genome = "GI:588489708"

handle=Entrez.efetch(db="sequences", id=gi_protein,rettype="fasta", retmode="text")
protein = SeqIO.parse(handle, "fasta").next()

handle=Entrez.efetch(db="sequences", id=gi_genome, rettype="gbwithparts", retmode="text")
genome = SeqIO.parse(handle, "gb").next()

#to extract feature with 'id' equal to protein
feature = [f for f in gb.features if "db_xref" in f.qualifiers and gi_protein in f.qualifiers["db_xref"]]

#to get location of CDS
start = feature[0].location.start.position
end = feature[0].location.end.position
strand = feature[0].location.strand 

seq = genome[start: end]

if strand == 1:
  print seq.seq
else:
  #if strand is -1 then to get reverse complement
  print seq.reverse_complement().seq

print protein.seq

然后你得到：

ATGGATTATATTGTTTCAGCACGAAAATATCGTCCCTCTACCTTTGTTTCGGTGGTAGGG
CAGCAGAACATCACCACTACATTAAAAAATGCCATTAAAGGCAGTCAACTGGCACACGCC
TATCTTTTTTGCGGACCGCGAGGTGTGGGAAAGACGACTTGTGCCCGTATCTTTGCTAAA
ACCATCAACTGTTCGAATATATCAGCTGATTTTGAAGCGTGTAATGAGTGTGAATCCTGT
AAGTCTTTTAATGAGAATCGTTCTTATAATATTCATGAACTGGATGGAGCCTCCAATAAC
TCAGTAGAGGATATCAGGAGTCTGATTGATAAAGTTCGTGTTCCACCTCAGATAGGTAGT
TATAGTGTATATATTATCGATGAGGTTCACATGTTATCGCAGGCAGCTTTTAATGCTTTT
CTTAAAACATTGGAAGAGCCACCCAAGCATGCCATCTTTATTTTGGCCACTACTGAAAAA
CATAAAATACTACCAACGATCCTGTCTCGTTGCCAGATTTACGATTTTAATAGGATTACC
ATTGAAGATGCGGTAGGTCATTTAAAATATGTAGCAGAGAGTGAGCATATAACTGTGGAA
GAAGAGGGGTTAACCGTCATTGCACAAAAAGCTGATGGAGCTATGCGGGATGCACTTTCC
ATCTTTGATCAGATTGTGGCTTTCTCAGGTAAAAGTATCAGCTATCAGCAAGTAATCGAT
AATTTGAATGTATTGGATTATGATTTTTACTTTAGGTTGGTGGATGCTTTTCTGGCAGAA
GATACTACACAAACACTATTGATTTTTGATGAGATATTGAAACGGGGATTTGATGCACAT
CATTTTATTTCCGGTTTAAGTTCTCATTTGCGTGATTTACTTGTATGTAAGGATGCAGCC
ACCATTCAGTTGCTGGATGTGGGTGCTAAAATTAAGGAGAAGTACGGTGTTCAGGCGCAA
AAAAGTACGATTGACTTTTTAATGGATGCTTTAAATATTACCAACGATTGCGATTTGCAA
TATAGGGTGGCTAAAAATAAGCGTTTGCATGTGGAGTTTGCTCTTCTTAAGATAGCACGT
GTATTAGATGAACAAAGAAAAAAGTAG

MDYIVSARKYRPSTFVSVVGQQNITTTLKNAIKGSQLAHAYLFCGPRGVGKTTCARIFAK
TINCSNISADFEACNECESCKSFNENRSYNIHELDGASNNSVEDIRSLIDKVRVPPQIGS
YSVYIIDEVHMLSQAAFNAFLKTLEEPPKHAIFILATTEKHKILPTILSRCQIYDFNRIT
IEDAVGHLKYVAESEHITVEEEGLTVIAQKADGAMRDALSIFDQIVAFSGKSISYQQVID
NLNVLDYDFYFRLVDAFLAEDTTQTLLIFDEILKRGFDAHHFISGLSSHLRDLLVCKDAA
TIQLLDVGAKIKEKYGVQAQKSTIDFLMDALNITNDCDLQYRVAKNKRLHVEFALLKIAR
VLDEQRKK

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