NCBI Taxon ID included in the final_table.tsv file? about pema

[hariszaf]

@cpavloud I found out about the ncbi-taxonomist tool.

We could use it I think.

Would you like to have a look and share any thoughts?

[cpavloud]

I am not sure how it would work exactly (the ncbi-taxonomist page does not provide very good examples/explanations), but we could give it a try.

[hariszaf]

Think of a while loop that will start from the end of the taxonomy in each row of the finalTable.tsv file and will use the ncbi-taxonomist for each level.
Using each level, we ll do queries searching for an ncbi taxonomy id, and when we have one we ll have something like this:

Assiming we are looking for Saprospiraceae

ncbi-taxonomist collect -n 'Saprospiraceae'

would return:

{"taxid":131567,"rank":"no rank","names":{"cellular organisms":"scientific_name"},"parentid":null,"name":"cellular organisms"}
{"taxid":2,"rank":"superkingdom","names":{"Bacteria":"scientific_name"},"parentid":131567,"name":"Bacteria"}
{"taxid":1783270,"rank":"clade","names":{"FCB group":"scientific_name"},"parentid":2,"name":"FCB group"}
{"taxid":68336,"rank":"clade","names":{"Bacteroidetes/Chlorobi group":"scientific_name"},"parentid":1783270,"name":"Bacteroidetes/Chlorobi group"}
{"taxid":976,"rank":"phylum","names":{"Bacteroidetes":"scientific_name"},"parentid":68336,"name":"Bacteroidetes"}
{"taxid":1937959,"rank":"class","names":{"Saprospiria":"scientific_name"},"parentid":976,"name":"Saprospiria"}
{"taxid":1936988,"rank":"order","names":{"Saprospirales":"scientific_name"},"parentid":1937959,"name":"Saprospirales"}
{"taxid":89374,"rank":"family","names":{"Saprospiraceae":"scientific_name","Saprospira group":"Synonym"},"parentid":1936988,"name":"Saprospiraceae"}

[cpavloud]

So, for example, if you have this classifications in the finalTable.tsv

Main genome;Eukaryota;Opisthokonta;Nucletmycea;Fungi;Dikarya;Ascomycota;Saccharomycotina;Saccharomycetes;Saccharomycetales;Dipodascaceae;Geotrichum

you would search for Geotrichum
and then for Dipodascaceae
and then for Saccharomycetales
etc etc.

and get the last line for each of your searches?

[hariszaf]

I would search for Geotrichum, if that has a hit, i d get

• only its ncbi taxonomy id
• the ncbi taxonomy ids of all its lineage
  we could think about that.

If I would not get a hit, I would continue with Dipodascaceae etc.

[hariszaf]

@cpavloud have a look. would that be ok ?

root@3bbfa77ef486:/mnt/analysis# more extenedFinalTable.tsv 
OTU	ERR0000001	Classification	TAXON:NCBI_TAX_ID
Otu4056	1	Main genome;Bacteria;Patescibacteria;Saccharimonadia;Saccharimonadales	Patescibacteria:1783273

[cpavloud]

@cpavloud have a look. would that be ok ?

root@3bbfa77ef486:/mnt/analysis# more extenedFinalTable.tsv 
OTU	ERR0000001	Classification	TAXON:NCBI_TAX_ID
Otu4056	1	Main genome;Bacteria;Patescibacteria;Saccharimonadia;Saccharimonadales	Patescibacteria:1783273

If there were no NCBI taxonomy IDs for Saccharimonadia and Saccharimonadales, I think we are fine :)

[hariszaf]

Exactly!
The thing is that there is not a ncbi taxonomy id always for a name in a ref db.
So i thought we could go up to the taxonomy found and work at one rank at a time starting from the species level.
I ll add this asap.

[hariszaf]

Just fyi, here is what you would get if you d search on ncbi taxonomy db for Saccharimonadales

and Saccharimonadia

[hariszaf]

This feature is now ready and will be part of pema:v.2.1.4.

The issue is now resolved.

[cpavloud]

Re-opening the issue:
In case it might be helpful, we can go from the sequence accession number to the NCBI Id: https://www.biostars.org/p/10959/

[hariszaf]

This is definitely useful for ITS #52