Biopython从全基因组中检索特定的CDS

2019年7月21日 197次阅读

我是Stackoverflow的新手.我正在尝试使用Bio
python自动化搜索过程.我有两个列表,一个具有蛋白质GI编号,另一个具有相应的核苷酸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对应于全基因组.我需要从与蛋白质GI匹配的每个基因组中检索特定的CDS.
我尝试使用不同的链接名称(“protein_nucleotide_cds”,“protein_nuccore”)再次使用ELink,但我得到的只是全基因组的id号.我应该尝试其他一些链接名称吗？
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())

该方法给出了fasta文件中的核苷酸和蛋白质序列,但核苷酸序列是全基因组.

如果有人能帮助我,我将非常感激.
提前感谢你！

最佳答案 我希望能帮助你

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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