Extracting multiple features using NCBI's e-utilities?
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6.3 years ago
ThePresident ▴ 180

I have a list of protein accession identifiers such as "CBE06962.1". I would like to automatically extract several features such as locus_tag, start and stop positions of the corresponding genes, UniProt tags etc. Is it possible to do it with by combining esearch and efetch from e-utilities, something like:

esearch -db protein -query "CBE06962.1" | efetch ???

If not, I am thinking of downloading all gbanks files and then parsing it for the info I want.

Any suggestions? Thanks in advance,

TP

e-utilities perl • 1.6k views
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6.3 years ago
GenoMax 144k

What about this report:

efetch -db protein -id "CBE06962.1" -format ipg

Id  Source  Nucleotide Accession    Start   Stop    Strand  Protein Protein Name    Organism    Strain  Assembly
18688109    INSDC   FN545816.1  3730243 3731418 -   CBE06962.1  sensor protein  Clostridioides difficile R20291 R20291  GCA_000027105.1
18688109    INSDC   FN538970.1  3649468 3650643 -   CBA66243.1  sensor protein  Clostridioides difficile CD196  CD196   GCA_000085225.1
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It's a good start, I can at least have the start/stop positions, the strand and nucleotide accession. One thing that would be really useful is a locus_tag.

Thanks, this is still pretty good though.

TP

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A single clean solution may be possible but at least this will get you started

efetch -db protein -id "CBE06962.1" -format gp | grep locus
                         /locus_tag="CDR20291_3124"

Since this brings back a GenPept format record you can grep for several other pieces of information.

efetch -db protein -id "CBE06962.1" -format gp | grep -e "locus" -e "coded"
                     /locus_tag="CDR20291_3124"
                     /coded_by="complement(FN545816.1:3730243..3731418)"
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Many thanks, this looks pretty good.

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