How to obtain taxonomic information from GIs

Question

[bpz]

Hi there

I think this might be an easy one, but I can't find a simple and fast way to do it. I have a fasta file with +1000 gis (I am constructing a phylogeny with these protein sequences), and I need to obtain the taxonomic information for each of them. Any ideas on how can I do this?

Thanks in advance.

[GenoMax]

No guarantee that this will work: Parsing Ncbi Taxonomic Tree?

Please be aware that gi numbers will be going away starting in September 2016.

Answer 1

[Brian Bushnell]

The BBMap package has a couple tools for doing this, described in bbmap/docs/guides/TaxonomyGuide.txt.

Essentially, after downloading the NCBI taxonomy files (described in the guide), they need to be converted to an efficient format using taxtree.sh and gitable.sh. Then can be used with taxonomy.sh. In your case, you would do this:

1) Download and unzip ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdmp.zip
2) Download ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_prot.dmp.gz
     (note: for nucleotides this would be ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_nucl.dmp.gz)
3) Convert them:
taxtree.sh names.dmp nodes.dmp tree.taxtree.gz
gitable.sh gi_taxid_prot.dmp.gz gitable.int1d.gz
4) Grab the headers from your fasta:
reformat.sh in=file.fasta out=names.header
5) Look at the taxonomy:
taxonomy.sh config=names.header table=gitable.int1d.gz tree=tree.taxtree.gz -da -Xmx1g

This will print one block per header which contains a gi number. Each block will look like this:

species 9606    Homo sapiens
genus   9605    Homo
family  9604    Hominidae
order   9526    Catarrhini
class   314146  Euarchontoglires
phylum  7711    Chordata
kingdom 33208   Metazoa
domain  2759    Eukaryota

...where the number signifies the NCBI taxID.

[bpz]

Hi Brian

Thanks a lot! , It is working alright... except the last bit, I can't find taxonomy.sh in my bbmap folder :p

[Brian Bushnell]

That's odd. What version do you have? I only added it fairly recently (in May), but I just downloaded the latest version (36.20) and verified that it is indeed present...

[bpz]

Ahh, yep, I think I have an older version. I am going to download the new one ASAP

[bpz]

I ran it, but I can't find the output. I got this message:

Loading tree.
Exception in thread "main" java.lang.RuntimeException: Can't find file /global/projectb/sandbox/gaag/bbtools/tax/tree.taxtree.gz
    at fileIO.ReadWrite.getRawInputStream(ReadWrite.java:815)
    at fileIO.ReadWrite.getGZipInputStream(ReadWrite.java:908)
    at fileIO.ReadWrite.getInputStream(ReadWrite.java:774)
    at fileIO.ReadWrite.readObject(ReadWrite.java:742)
    at fileIO.ReadWrite.read(ReadWrite.java:1090)
    at tax.PrintTaxonomy.<init>(PrintTaxonomy.java:137)
    at tax.PrintTaxonomy.main(PrintTaxonomy.java:40)

[Brian Bushnell]

Hmm, can you show me the command line? By default it is supposed to look in that hard-coded location only if you did not specify a path to the taxtree file you generated in step 3.

[bpz]

OK, is this one:

./taxonomy.sh config=names.header table=gitable.int1d.gz tree=tree.taxtree.gz -da -Xmx1g

[Brian Bushnell]

Ah, sorry, looks like there's a bug. "config=names.header" is overwriting your other flags. I will fix that. For now, can you edit the config file to add these two lines:

table=gitable.int1d.gz
tree=tree.taxtree.gz

Then run the same command again. Please let me know if that works!

[bpz]

Sorry, I can't find the config file. Where is it exactly?, do I add the lines at the end?

[Brian Bushnell]

By "config file" I mean "names.header", sorry :) And yes, just add those lines at the beginning or end.

[bpz]

Hello again

It didn't work unfortunately, the error message is:

Loading gi table.
Loading tree.
Exception in thread "main" java.lang.RuntimeException: java.io.InvalidClassException: tax.TaxTree; local class incompatible: stream classdesc serialVersionUID = -6216551978806194900, local class serialVersionUID = 1682832560435175041
    at fileIO.ReadWrite.readObject(ReadWrite.java:751)
    at fileIO.ReadWrite.read(ReadWrite.java:1090)
    at tax.PrintTaxonomy.<init>(PrintTaxonomy.java:137)
    at tax.PrintTaxonomy.main(PrintTaxonomy.java:40)
Caused by: java.io.InvalidClassException: tax.TaxTree; local class incompatible: stream classdesc serialVersionUID = -6216551978806194900, local class serialVersionUID = 1682832560435175041
    at java.io.ObjectStreamClass.initNonProxy(ObjectStreamClass.java:616)
    at java.io.ObjectInputStream.readNonProxyDesc(ObjectInputStream.java:1630)
    at java.io.ObjectInputStream.readClassDesc(ObjectInputStream.java:1521)
    at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1781)
    at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1353)
    at java.io.ObjectInputStream.readObject(ObjectInputStream.java:373)
    at fileIO.ReadWrite.readObject(ReadWrite.java:747)
    ... 3 more

[Brian Bushnell]

Sorry for all of the complication. That's because you processed the initial files with an older version of BBMap and I changed the format of the taxtree file in the newer version; it will need to be regenerated:

taxtree.sh names.dmp nodes.dmp tree.taxtree.gz

[bpz]

Hello again

Sorry for the inconvenience. Now when I run "taxonomy.sh" I get this message:

Loading tree.
Exception in thread "main" java.lang.RuntimeException: Can't find file /global/projectb/sandbox/gaag/bbtools/tax/tree.taxtree.gz
    at fileIO.ReadWrite.getRawInputStream(ReadWrite.java:815)
    at fileIO.ReadWrite.getGZipInputStream(ReadWrite.java:908)
    at fileIO.ReadWrite.getInputStream(ReadWrite.java:774)
    at fileIO.ReadWrite.readObject(ReadWrite.java:742)
    at fileIO.ReadWrite.read(ReadWrite.java:1090)
    at tax.PrintTaxonomy.<init>(PrintTaxonomy.java:137)
    at tax.PrintTaxonomy.main(PrintTaxonomy.java:40)

[GenoMax]

Can't find file /global/projectb/sandbox/gaag/bbtools/tax/tree.taxtree.gz

That file is not in that directory. Provide an alternate path/dir as needed.

[Brian Bushnell]

In this case, that's the default directory, harded-coded so that people at JGI won't have to add it, and it's not supposed to be used elsewhere, but apparently there's a bug. I'll fix it very soon; possibly tomorrow. Did you get this exception even though you put the lines

table=gitable.int1d.gz
tree=tree.taxtree.gz

in the names.header file?

[bpz]

Yep, I added the lines and still got that exception.

[Brian Bushnell]

OK! Sorry about that, I will post a fixed version tomorrow.

[erik.hjerde]

Hi, Was there a solution to this? My attempts also ends here: Can't find file /global/projectb/sandbox/gaag/bbtools/tax/tree.taxtree.gz

I am using version 37.78 Best, Erik

Answer 2

[natasha.sernova]

I would recommend two step-way:

1a)Convert your gi numbers to accession numbers:

With this perl-script below:

http://bioinformatics.cvr.ac.uk/blog/convert-ncbi-protein-gi-to-genome-accession/

or differently:

1b)From this site

http://www.ncbi.nlm.nih.gov/books/NBK25501/

go here

http://www.ncbi.nlm.nih.gov/books/NBK25498/#chapter3.Application_1_Converting_GI_num

and then follow this post (second step for any a) or b) starts):

Automatically Getting The Ncbi Taxonomy Id From The Genbank Identifier

BTW, Neilfws recommended a direct way from Gi to taxID, so there are many possible choices.