Extract NCBI's refseq assembly accession number from nuccore IDs

Question

[genomes_and_MGEs]

Hey guys,

I have a list of nuccore IDs in a text file (let's call it file.txt), and want to append the NCBI's refseq assembly accession number next to the nuccore ID, such as this

GCF_000006765.1_NC_002516.2

I've tried with the following command, but only the NCBI's refseq assembly accession number shows up

for file in $(cat file.txt) ; do esearch -db nuccore -query "$file" | elink -db assembly -target assembly | esummary | xtract -pattern DocumentSummary -element Caption,AssemblyAccession,BioSample >> GCFs_nucl_accessions.txt; done

Can you help me out? Thanks!

[Michael]

What if there was no assembly for a nucleotide sequence?

[genomes_and_MGEs]

All the nucleotide IDs I have correspond to either the chromosome or plasmids from complete bacterial genomes, so I expect each ID will have a corresponding assembly accession.

[Michael]

Ok, your query was fine, I think I fixed the shell code so it works as expected now.

[GenoMax]

This is the assembly database record for the ID included above. Are you looking to get NC* id based on the GCF ID? GCF ID's are RefSeq ID's by the way they are not nuccore ID's.

[genomes_and_MGEs]

I have a list of NC* IDs, and want to append the corresponding GCF ID to each one.

[GenoMax]

Please post more than one example. It is always good to do this when you ask questions about ID's. You can simply do this to get the GCF ID:

$ esearch -db assembly -query "NC_002516.2"  | esummary | xtract -pattern DocumentSummary -element RefSeq
GCF_000006765.1

[genomes_and_MGEs]

Sure, here's the top 5 IDs

NC_002774.1
NC_003140.1
NC_005951.1
NC_006625.1
NC_007790.1

Answer 1

[GenoMax]

Using EntrezDirect:

$ more id

NC_002774.1
NC_003140.1
NC_005951.1
NC_006625.1
NC_007790.1

$ for i in `cat id`; do printf ${i}"\t"; esearch -db assembly -query ${i}  | esummary | xtract -pattern DocumentSummary -element RefSeq; done
NC_002774.1 GCF_000009665.1
NC_003140.1 GCF_000009645.1
NC_005951.1 GCF_000011525.1
NC_006625.1 GCF_000009885.1
NC_007790.1 GCF_000013465.1

You can change the printed output as needed to concatenate the ID's the way you want them.

Answer 2

[Michael]

Your shell code was almost correct, try the following:

for file in $(cat file.txt) ; do
   echo $(esearch -db nuccore -query "$file" | \
   elink -db assembly -target assembly | \
   esummary | xtract -pattern DocumentSummary -element \ 
   Caption,AssemblyAccession,BioSample)_$file >> 
   GCFs_nucl_accessions.txt;
done

[genomes_and_MGEs]

Thanks for sharing this, but at least for me the code doesn't work exactly as expected; it outputs

-bash: GCF_000009665.1_NC_002774.1: command not found
-bash: GCF_000009645.1_NC_003140.1: command not found
...