Downloading Batch Entrez Protien Information

Question

[Andrew]

I am trying to download a large amount of NCBI entries from a large set of accession numbers returned by a blastp search. With my list of accession numbers, I am looking for their taxonomy, bacteria, or virus, which is available when using batch entrez in protein search and downloading the returned list in GenPept format. Where I am having an issue is that some of these numbers are flagged by batch entrez as, Id=MBG9901843.1: protein: Wrong UID MBG9901843.1 which is about 230 out of a 2500 set of accession numbers. Those that are flagged in this manner do get returned when using the Identical Protein Group entrez option, however, I would have to switch the format to Genpept one by one and download them one by one. Is there a simpler way to obtain the taxonomy of an accession number from a list of accessions? I would simply ignore those that get flagged as the Wrong UID however it cuts out too much of the data for my liking. I know this is a bit of a long-winded explanation and I'll be glad to clarify any aspect.

[xuongsanxuatnoithathometalk]

Thanks you very mmuch

Answer 1

[GenoMax]

See: NCBI Accession Number to Taxonomy ID

Using EntrezDirect:

$ esummary -db ipg -id MBG9901843 | xtract -pattern DocumentSummary -element Caption,TaxId,Organism,Div
MBG9901843      293387  Bacillus altitudinis    BCT

For more than one ID, put them in a file, one per line (here id):

$ more id
MBG9901560
MBG9901570
MBG9901580
MBG9901843

$ for i in `cat id`; do esummary -db ipg -id ${i} | xtract -pattern DocumentSummary -element Caption,TaxId,Organism,Div; done
WP_008343464    1386    Bacillus        BCT
WP_007497670    2       Bacteria        BCT
WP_017360045    1386    Bacillus        BCT
MBG9901843      293387  Bacillus altitudinis    BCT

[Andrew]

Great, thank you so much!

[Andrew]

Have there been any known issues with the files transmute.Linux.gz, xtract.Linux.gz, and rchive.Linux.gz on download of EntrezDirect? I seem to have at least one of these become corrputed and not unzipped on each install.

[GenoMax]

If you are on macOS:

Download these files manually from the NCBI EntrezDirect ftp site: http://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/

Extract files: gunzip -f *.gz

Change permission using chmod +x for all 3 files.