Question: Counting a number of mobile elements in a list of genomes using BioPython
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gravatar for little_more
6 months ago by
little_more10
little_more10 wrote:

Suppose I have a big list of assembly IDs:

['GCA_000005845.2',  'GCA_000006925.2',  'GCA_000007405.1',  'GCA_000007445.1', ...]

And I need to count a number of mobile elements in each chromosome in all assemblies. How could I do this using BioPython? It seems that I need to download all genbank files and count mobile elements by parsing each one of them. Unfortunately, I can't find a function to download a full genbank file given an assembly ID.

I tried to do this since the direct search for "GCA_000005845.2" in assembly db doesn't work:

Entrez.email = "" # Always tell NCBI who you are
handle = Entrez.esearch(db="assembly", term="GCA_000005845.2")
record = Entrez.read(handle)
handle1=Entrez.esummary(db="assembly",id=record['IdList'], report="full")
print(Entrez.read(handle1))

But I don't know what to do next as the result does not contain GenBank ID (U00096.3). So is there a way to do this with BioPython or maybe someone knows another simple way?

biopython genome • 184 views
ADD COMMENTlink written 6 months ago by little_more10
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