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.
2 answers
I'm too lazy to write an XSLT stylesheet, but that could be a solution.
e.g.: see my previous answer for this question
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.
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