How to get summary for acc.no. not starting with 'WP_' ?

Hi Biostars community,

I want to use epost and esummary (NCBIs eutils) to obtain information on the lineage.

But I have some problems with accession numbers not starting like WP_.

While

cat "$ListWithAccessionNumbers" | epost -db protein |\
    esummary -db taxonomy -format xml | \
    xtract  -pattern Seq-entry -element Org-ref_taxname, OrgName_lineage, NCBIeaa, Textseq-id_accession \
    > SummaryTable.tsv

gives me a tsv file indeed, some cells are not filled with the requested information.

For the accession numbers not starting with WP_ the accession number and sequence are not printed out, this will only be printed for the accession numbers starting with WP_.

So my current question is how can I obtain lineage information for those accession numbers using epost and esummary that do not start with WP_ but still also get the accession number and sequence printed out? Is there anyone with experience regarding this?

If though you have some suggestions on how to use epost and esummary differently instead or know of an alternative way of using the NCBIs e-utilities to solve this problem, I am grateful for your ideas and help! Thank you!

esummary epost lineage summary e-utility

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updated 5.7 years ago by Ram

• written 5.7 years ago by 6schulte •

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.
code_formatting

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written 5.7 years ago by Ram

Thank you! I didn't know that, very helpful :)

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written 5.7 years ago by 6schulte •

1 answer

So my current question is how can I obtain lineage information for those accession numbers using epost and esummary that do not start with WP_ but still also get the accession number and sequence printed out? I

Once an input is passed to Entrezdirect there is no way to keep track of it. So you should print it before it gets passed to Entrezdirect.

Edit: Taking out code which was not tested. Use @vkkodali's solution which is complete.

If that information is missing for specific accessions, you are not going to get that.

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written 5.7 years ago by GenoMax

Just noting that you are not parsing taxonomy XMLs. The output piped from esearch already is using the protein database and esummary ignores -db taxonomy in this instance. If you want to do cross-database searches you will need to use elink. If all you need is taxonomy info (and not sequence) you can do something like:

for i in `cat file_w_accession_one_per_line`; do 
    printf ${i}"\t"; \
    epost -db protein -id ${i} -format acc \
    | elink -target taxonomy \
    | efetch -format xml \
    | xtract -pattern TaxaSet -first ScientificName -element Lineage ;
done > SummaryTable.tsv

If on the other hand, you want the sequence as well, you can simplify it to:

for i in `cat file_w_accession_one_per_line`; do 
    printf ${i}"\t"; \
    efetch -db protein -id ${i} -format xml \
    | xtract -pattern Seq-entry -element Org-ref_taxname, OrgName_lineage, NCBIeaa, Textseq-id_accession ;
done > SummaryTable.tsv

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written 5.7 years ago by vkkodali_ncbi

Thank you for your reply genomax, You have already helped me with my last question. And I am sorry for not giving an example on what acc. no. I am working with... WP_112675856, CCH19814, WP_149273991, RSN10899 would be examples.

And thank you, vkkodali, very much as well! The suggested code works pretty good! :) The code suggested for also retreving the sequence unfortunately does not print the sequence for acc. no. like: CCH19814 and RSN10899. But only for the ones like WP_112675856, and WP_149273991.

Because of that I can extract the sequence with an easy esl-sfetch command and do not neccessaryly need it right now I will just work with the code you suggested as first option. Thank you!

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written 5.7 years ago by 6schulte •