This new tool is now live on the main Tool Shed: http://toolshed.g2.bx.psu.edu/view/peterjc/align_back_trans
Peter On Tue, Feb 18, 2014 at 2:10 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > Hi all, > > If anyone is interested, I've just wrapped a little Python script > I'd prepared early for use in Galaxy for a fairly common need - > "back translating" a protein alignment into a nucleotide alignment > by threading the unaligned sequence. > > We're testing this locally, and barring any major issues I > would expect to release this to the main Tool Shed in a week > or so - but if any of you want to have a play with it now, and > pass on feedback, please do so: > > Development repository: > https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans > > Test Tool Shed release: > http://testtoolshed.g2.bx.psu.edu/view/peterjc/align_back_trans > > Planned Tool Shed release: > http://toolshed.g2.bx.psu.edu/view/peterjc/align_back_trans (pending) > > This uses Biopython's AlignIO [*] module and so can handle a > range of alignment file formats - for now I have restricted this > to "fasta", "clustal" and "phylip" which I believe are all already > in use on the tool shed - there is probably scope here for a > more coordinated effort to define Galaxy datatypes in this > area, including things like the PFAM/Stockholm format and > strict/relaxed variants of PHYLIP. > > Regards, > > Peter > > [*] http://biopython.org/wiki/AlignIO ___________________________________________________________ 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/
