Re: [galaxy-dev] Pick-you-own columns in BLAST+ tabular output
On Tue, Mar 4, 2014 at 12:19 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Tue, Mar 4, 2014 at 10:35 AM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Peter, Hello all, I've mentioned before that a forthcoming update to the BLAST+ Galaxy wrappers would be adding a most customisable output option with pick-your-own columns. This is available to test now from the Test Tool Shed, along with other enhancements like more masking tools and an update to BLAST+ 2.2.29: http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus ... Some community testing/comments would be appreciated. I tested it briefly on my test instance and it looks all fine and seems to work :) Thanks, looking forward to see it in MainTS. Bjoern Great - thanks. I'm about to update our local production server, and barring any problems will push this BLAST+ update to the main Tool Shed later this week. This is now live, with a regression about output formats caught and fixed: http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus 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/
Re: [galaxy-dev] Pick-you-own columns in BLAST+ tabular output
Hi Peter, Hello all, I've mentioned before that a forthcoming update to the BLAST+ Galaxy wrappers would be adding a most customisable output option with pick-your-own columns. This is available to test now from the Test Tool Shed, along with other enhancements like more masking tools and an update to BLAST+ 2.2.29: http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus (This will be released as the ncbi_blast_plus wrappers v0.1.0, and includes recent contributions from Jim Johnson and Björn Grüning - thank you both): Previously (for tabular output) we've only offered the standard 12 column output (-outfmt 6), and an extended set which has grown to currently include 25 columns. The new custom column mode offers the 12 standard columns, and the extended set (making 25 columns), plus other (to me less interesting) identifiers, some other miscellaneous columns, and the taxonomy columns (44 columns in all): [image: Inline image 1] [image: Inline image 2] As previously discussed, the list of columns has been grouped - the first two groups reflect the standard 12 columns and the columns used in Galaxy's (default) 25 column extended tabular output. The remaining columns I have split into three groups (assorted identifiers, miscellaneous, and taxonomy) which I hope is self explanatory. Note that this does *not* allow you pick the column order - they will be produced in the order shown. The underlying BLAST+ tools would support this, but the Galaxy GUI would I feel be too complicated. I think that is fine, I can't imagine of any real use case where that is needed. Some community testing/comments would be appreciated. I tested it briefly on my test instance and it looks all fine and seems to work :) Thanks, looking forward to see it in MainTS. Bjoern Thanks, 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/
Re: [galaxy-dev] Pick-you-own columns in BLAST+ tabular output
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-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@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-split.png (Screenshot from this thread last month, where opinion was split) http://dev.list.galaxyproject.org/Including-descriptions-etc-in-extended-BLAST-tabular-output-tc4662704.html 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/ ___ 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/
