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pjotrp / blastxmlparser

Fast big data XML parser and library, written in Ruby
MIT License
17 stars 3 forks source link

New BLAST XML format #4

Open pjotrp opened 9 years ago

pjotrp commented 9 years ago

The NCBI is now making a new version of the BLAST XML available for testing. Read about the changes and how to access BLAST results using the new XML at ftp://ftp.ncbi.nlm.nih.gov/blast/documents/NEWXML/xml2.pdf

Anyone an interest in this?

n8upham commented 9 years ago

Yes for sure, I'm interested— especially for the use of taxids within the more-easily parsable XML format. Is it already implemented anywhere? Thanks

pjotrp commented 9 years ago

@n8upham send me an E-mail and we can discuss. Taxids were sorely missing, indeed.

n8upham commented 9 years ago

Hi there Yes, do you know if the new XML format is (a) up and running, and (b) use-able from the UNIX executable (2.2.31+ now)? My aim for the XML output is to be able to use biopython’s blast-based tools for parsing. But right now the option “5” seems to still output regular XML (i.e., without the taxis, which I am keen to use)

Thanks much —nate

On Jun 24, 2015, at 3:18 AM, Pjotr Prins notifications@github.com wrote:

@n8upham https://github.com/n8upham send me an E-mail and we can discuss. Taxids were sorely missing, indeed.

— Reply to this email directly or view it on GitHub https://github.com/pjotrp/blastxmlparser/issues/4#issuecomment-114758991.