I have a bunch of refseq assembly genome number likeGCF_002514765.1,GCF_002485085.1,GCF_002201835.1,GCF_000593305.2,GCF_001887655.1,GCF_000194215.1,GCF_002098145.1,GCF_002807875.1
Now I want to use these to search which genome it is , for example, the first one is Escherichia coli strain MOD1-EC3823, I try to use efetch to achieve this, but seems it does not work, it says "urllib.error.HTTPError: HTTP Error 400: Bad Request" here is my python code:
from Bio import Entrez
Entrez.email = "hulala@gmail.com"
ID = open("assembly_ID").read()
handle = Entrez.efetch(db="assembly", id= ID, rettype="gb")
print(handle.read())
Does anyone have any idea?
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written
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horsedog •
Re-writting the following query in python should get you what you want:
esearch -db assembly -query "GCF_002514765.1" | esummary | xtract -pattern DocumentSummary -element SpeciesName Sub_type Sub_value
The output is:
Escherichia coli strain MOD1-EC3823
Hi , thanks , but it says "SyntaxError: invalid syntax" at Sub_value
do you mean by replacing
ID = open("assembly_ID").read()
handle = Entrez.efetch(db="assembly", id= ID, rettype="gb")
by your code? but here the -query is not just one ID, there are thousands of
you will need to do a loop in your python code to query each accession one at a time.
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