How to get all chromosomes RefSeq ID from RefSeq assembly ID?

Question

[Maria]

I have a RefSeq assembly accession ID from an organism that has two chromosomes. I want to retrieve from NCBI the RefSeq chromosomes IDs and their lengths in base pairs.

I have been trying to use Entrez in python:

from Bio import Entrez
Entrez.email = "my@email"
handle = Entrez.esummary(db="assembly", term=RefSeq_assembly_accession)
summary = Entrez.read(handle)

but many times there seem to not found any assembly for the provided accession, nevertheless when I manually look it up in the NCBI webpage, the assembly is there.

Example: I have the following RefSeq assembly accession ID RefSeq_assembly_accession="GCF_030718785.1"

I would like to retrieve: chromosome_1= "NZ_CP132190.1" chromosome_1_size= 2,959,192 chromosome_2= "NZ_CP132189.1" chromosome_2_size=1,107,495

NCBI record for this example: https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_030718785.1/

Any help would be greatly appreciated! Thanks :)

Answer 1

[GenoMax]

Using datasets/dataformat command line utils (LINK) :

$ datasets summary genome accession GCF_030718785.1 --report sequence --as-json-lines | dataformat tsv genome-seq --fields accession,genbank-seq-acc,refseq-seq-acc,chr-name,mol-type,seq-length

Assembly Accession      GenBank seq accession   RefSeq seq accession    Chromosome name Molecule type   Seq length
GCF_030718785.1 CP132190.1      NZ_CP132190.1   1       Chromosome      2959192
GCF_030718785.1 CP132189.1      NZ_CP132189.1   2       Chromosome      1107495