Hello all, For those interested in more flexible tabular output from BLAST+, please try out the wrappers on the *Test* Tool Shed which I have also just updated to wrap BLAST+ 2.2.29 as well: http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus One open question is should the interface for picking columns include the current column numbers or not? e.g. http://dev.list.galaxyproject.org/attachment/4662771/0/blast-pyo-columns-spl... (Screenshot from this thread last month, where opinion was split) http://dev.list.galaxyproject.org/Including-descriptions-etc-in-extended-BLA... In future work we'll add some of the new columns added in the BLAST+ 2.2.28 release like taxonomy fields - but this needs a bit of thought about how to handle the taxonomy database (i.e. should we support multiple versions for full reproducibility, or just use the current version on disk regardless). Most of the time updates to the NCBI taxonomy will simply be additions, which should be harmless to reproducibility - but sometimes taxa can be rearranged. https://github.com/peterjc/galaxy_blast/issues/20 https://github.com/peterjc/galaxy_blast/issues/21 Regards, Peter
Peter, We will definitely give them a try. I never understood why the tabular outputs did have an option to include the defline/hit decription. Just for that we needed to use the cloggy XML output and parse that into a table again. Conserved header names are more useful to us than having column numbers. But either is fine with us. Alex -----Oorspronkelijk bericht----- Van: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] Namens Peter Cock Verzonden: woensdag 15 januari 2014 11:54 Aan: galaxy-dev@lists.bx.psu.edu Onderwerp: [galaxy-dev] Pick-you-own columns in BLAST+ tabular output Hello all, For those interested in more flexible tabular output from BLAST+, please try out the wrappers on the *Test* Tool Shed which I have also just updated to wrap BLAST+ 2.2.29 as well: http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus One open question is should the interface for picking columns include the current column numbers or not? e.g. http://dev.list.galaxyproject.org/attachment/4662771/0/blast-pyo-columns-spl... (Screenshot from this thread last month, where opinion was split) http://dev.list.galaxyproject.org/Including-descriptions-etc-in-extended-BLA... In future work we'll add some of the new columns added in the BLAST+ 2.2.28 release like taxonomy fields - but this needs a bit of thought about how to handle the taxonomy database (i.e. should we support multiple versions for full reproducibility, or just use the current version on disk regardless). Most of the time updates to the NCBI taxonomy will simply be additions, which should be harmless to reproducibility - but sometimes taxa can be rearranged. https://github.com/peterjc/galaxy_blast/issues/20 https://github.com/peterjc/galaxy_blast/issues/21 Regards, Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
On Fri, Jan 17, 2014 at 8:34 AM, Bossers, Alex <alex.bossers@wur.nl> wrote:
Peter, We will definitely give them a try.
Great.
I never understood why the tabular outputs did have an option to include the defline/hit decryption.
That was a long standing gripe of mine too, fixed in BLAST+ 2.2.28 and available in the BLAST+ wrappers on the main Tool Shed since Dec 2013, http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/ - see also: http://blastedbio.blogspot.co.uk/2012/05/blast-tabular-missing-descriptions....
Just for that we needed to use the cloggy XML output and parse that into a table again.
Yes, that was a pain. It was the main reason for writing this tool: http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
Conserved header names are more useful to us than having column numbers. But either is fine with us. Alex
Yes, I'd also like the standard BLAST+ tabular output to include a # (hash) commented header line listing the fields (tab separated). They do something like this in the extremely verbose commend tabular output, but that adds a lot of other largely redundant comment lines as well :( Regards, Peter
participants (2)
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Bossers, Alex -
Peter Cock