Question: To retrieve bacterial Phylum and Class information from a set of tax id
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gravatar for sinumolgeorge
5 months ago by
sinumolgeorge0 wrote:

Hi ,

I wanted to get the phylum and class information of set of species , its about 1000 . I have each tax id . Is there any possibility to get the phylum and class information by uploading the tax id file in a batch search?

snp rna-seq sequence next-gen gene • 271 views
ADD COMMENTlink modified 5 months ago by Brian Bushnell15k • written 5 months ago by sinumolgeorge0
0
gravatar for Pierre Lindenbaum
5 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum104k wrote:

download the NCBI taxdump file from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdmp.zip , unzip the content , sort, and join the files & get the result.

see ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump_readme.txt for a description of the content of the zip file

ADD COMMENTlink modified 5 months ago • written 5 months ago by Pierre Lindenbaum104k

It contains several files with .dmp extension. Can i join all these

ADD REPLYlink written 5 months ago by sinumolgeorge0
0
gravatar for Joseph Hughes
5 months ago by
Joseph Hughes2.5k
Scotland, UK
Joseph Hughes2.5k wrote:

You could use NCBI eutilities with esarch and efetch. From the xml output you can extract the full lineage:

esearch -db taxonomy -query "txid11053 [Organism]" | efetch -format xml | xtract -element Lineage
ADD COMMENTlink written 5 months ago by Joseph Hughes2.5k

ERROR: No -pattern in command-line arguments

ADD REPLYlink written 5 months ago by sinumolgeorge0
1

Try searching with the -pattern parameter.

esearch -db taxonomy -query "txid11053 [Organism]" | efetch -format xml | xtract  -pattern Lineage -element Lineage
ADD REPLYlink written 4 months ago by Sej Modha2.6k
0
gravatar for Brian Bushnell
5 months ago by
Walnut Creek, USA
Brian Bushnell15k wrote:

You can also query this URL with a comma-delimited list of numbers. For example:

http://taxonomy.jgi-psf.org/tax/id/9606,1234

ADD COMMENTlink written 5 months ago by Brian Bushnell15k
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