Search using Entrez and return accession numbers (not GI)

Question

[Cricket]

I am trying to use Biopython (Entrez) with search terms that will return the accession number (and not the GI*).

Here is a tiny excerpt of my code:

from Bio import Entrez

Entrez.email = 'myemailaddress'
search_phrase = 'Escherichia coli[organism]) AND (complete genome[keyword])'
handle = Entrez.esearch(db='nuccore', term=search_phrase, retmax=100, rettype='acc', retmode='text')
result = Entrez.read(handle)
handle.close()
gi_numbers = result['IdList']
print(gi_numbers)

'745369752', '910228862', '187736741', '802098270', '802098269', '802098267', '387610477', '544579032', '544574430', '215485161', '749295052', '387823261', '387605479', '641687520', '641682562', '594009615', '557270520', '313848522', '309700213', '284919779', '215263233', '544345556', '544340954', '144661', '51773702', '202957457', '202957451', '172051323'

What slice of magic am I missing? Thank you for your assistance.

*especially since they are phasing out GI numbers

Answer 1

[Alexander Goncearenco]

Eutils esearch does not return complete records. You will need efetch for that. Continuing your lines of code:

from Bio import Entrez

Entrez.email = 'myemailaddress'
search_phrase = 'Escherichia coli[organism]) AND (complete genome[keyword])'
handle = Entrez.esearch(db='nuccore', term=search_phrase, retmax=100, rettype='acc', retmode='text')
result = Entrez.read(handle)
handle.close()
gi_numbers = result['IdList']

h = Entrez.efetch(db="nucleotide", id=gi_numbers, rettype="acc")
h.read().splitlines()
h.close()

['HF572917.2', 'NZ_HF572917.1', 'NC_010558.1', 'NZ_HG941720.1', 'NZ_HG941719.1', 'NZ_HG941718.1', 'NC_017633.1', 'NC_022371.1', 'NC_022370.1', 'NC_011601.1', 'NZ_HG738867.1', 'NC_012892.2', 'NC_017626.1', 'HG941719.1', 'HG941718.1', 'HG941720.1', 'HG738867.1', 'AM946981.2', 'FN649414.1', 'FN554766.1', 'FM180568.1', 'HG428756.1', 'HG428755.1', 'M37402.1', 'AJ304858.2', 'FM206294.1', 'FM206293.1', 'AM886293.1', '']

Alternatively, install eutils and run:

$ esearch -db nuccore -query "(Escherichia coli[organism]) AND (complete genome[keyword])" |efetch -mode text -format acc

HF572917.2 NZ_HF572917.1 NC_010558.1 NZ_HG941720.1 NZ_HG941719.1 NZ_HG941718.1 NC_017633.1 NC_022371.1 NC_022370.1 NC_011601.1 NZ_HG738867.1 NC_012892.2 NC_017626.1 HG941719.1 HG941718.1 HG941720.1 HG738867.1 AM946981.2 FN649414.1 FN554766.1 FM180568.1 HG428756.1 HG428755.1 M37402.1 AJ304858.2 FM206294.1 FM206293.1 AM886293.1

[Whetting]

that works great! However, with NCBI getting rid of GI numbers soon, this will stop working soon, right?