How to fill taxonomy informations from NCBI?

Question

[Camp]

Hi, there!

I've seen questions related to that but none addressing in with lay explanations which is very much indeed my case. I have about 500 species list to fill with Kingdom, Phylum, Class, Order, Family

I saw that i should follow something such as "specie OR specie OR..." in NCBI taxonomy > Display setting > common tree > Save as

When i save this it just gives me a messy information in all one column

I looked for simple tutorials, scripts but didnt find any

Would love and deeply appreciate some help for a lay person!

Answer 1

[MSRS]

Step 1

Use NCBI Taxonomy browser to convert species name to corresponding Taxonomy ID.

Step 2

Use TaxonKit to convert related lineage detail (Phylum, class, order,....species) of those TaxId

taxonkit lineage id.txt | tee lineage.txt

Step 3

Use csvtk to formating these lineage.

cat lineage.txt \
    | taxonkit reformat \
    | csvtk -H -t cut -f 1,3 \
    | csvtk -H -t sep -f 2 -s ';' -R \
    | csvtk add-header -t -n taxid,kindom,phylum,class,order,family,genus,species \
    | csvtk pretty -t > out_id.txt

Thank you

[shenwei356]

taxonkit reformat supports input of TaxIds (since v0.8.0) and recognizes "\t" in output format. Therefore, it can be simplified as:

taxonkit name2taxid names.txt \
    | taxonkit reformat -I 2 -f "{k}\t{p}\t{c}\t{o}\t{f}\t{g}\t{s}" -o result.txt

Add header and save to XLSX format if you like:

taxonkit name2taxid names.txt \
    | taxonkit reformat -I 2 -f "{k}\t{p}\t{c}\t{o}\t{f}\t{g}\t{s}" \
    | csvtk add-header -t -n "name,taxid,kindom,phylum,class,order,family,genus,species" \
    | csvtk csv2xlsx -t -o result.xlsx

Answer 2

[GenoMax]

See answers here:

Convert list of Accession Numbers to Full Taxonomy
converting taxID to taxonomy

If this does not help solve your problem provide examples of species names.