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/
