Hi all, I was just surprised to find what I consider to be a major bug in fasta_to_tabular_converter.py used to convert FASTA into tabular.
Consider this toy example: >alpha ACGTAC >beta AGTGTA >gamma with some description AGGTACCA What the converter gives is two columns (title line and sequence), but the '>' is left in: >alpha (tab) ACGTAC >beta (tab) AGTGTA >gamma with some description (tab) AGGTACCA Given just two columns, what I was expecting was: alpha (tab) ACGTAC beta (tab) AGTGTA gamma with some description (tab) AGGTACCA I think this is a bug. In support of this view, I note the user-facing (now in the Tool Shed) removes the '>' symbol: https://toolshed.g2.bx.psu.edu/view/devteam/fasta_to_tabular https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular I have submitted a pull request to address this: https://github.com/galaxyproject/galaxy/pull/11 Note what I really wanted was three columns, the ID, comment and sequence: alpha (tab) (empty) (tab) ACGTAC beta (tab) (empty) (tab) AGTGTA gamma (tab) with some description (tab) AGGTACCA The user-facing tool does support this. I appreciate that changing the built-in implicit converter to give three column output could be a problem for backward compatibility (if anyone has written a workflow using the '>' version of the implicit conversion?), so I can make this conversion explicit in my workflow. 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/