Ncbi Xml To Gff/Gtf

Question

[Darked89]

I started with: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ASN_BINARY/Mammalia/Sus_scrofa.ags.gz

and converted it to XML: ./gene2xml.linux -i Sus_scrofa.ags -b T -c T

(gene2xml.linux from ftp://ftp.ncbi.nlm.nih.gov/asn1-converters/by_platform/linux/gene2xml.linux.gz)

Are you aware of any tools to make such conversion?

I am OK with a simplistic GFF with gene-transcript-exons info only.

Answer 1

[Pierre Lindenbaum]

I'm too lazy to write an XSLT stylesheet, but that could be a solution.

e.g.: see my previous answer for this question

Answer 2

[Daniel Standage]

I recently sent this question to the NCBI help desk directly, and this is the response I got.

Hello,

There are some conversion utilities on the Gene FTP site:

ftp://ftp.ncbi.nih.gov/gene/tools/

See the README there for details.

However, the conversion from the NCBI XML to GFF3 didn't seem at all straightforward. Since it appears that I suffer from the same laziness issue that Pierre has, I ended up finding another way to get the data I needed without converting from the XML.