Changing fasta_to_tabular_converter.py

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Changing fasta_to_tabular_converter.py

Peter Cock
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
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