i can't find this comment outside of my email for some reason. are you
suggesting to always compute md5 and then suppress in the output via
command?


On Thu, Aug 15, 2013 at 2:26 PM, Jai Ram Rideout
<notifications@github.com>wrote:

> In python-code/biom/commands/summarize_biom_table.py:
>
> > +__credits__ = ["Greg Caporaso"]
> > +__license__ = "GPL"
> > +__version__ = "1.1.2-dev"
> > +__maintainer__ = "Greg Caporaso"
> > +__email__ = "gregcaporaso@gmail.com"
> > +
> > +class SummarizeBiomTable(Command):
> > +    """
> > +     Example usage:
> > +      from biom.commands.summarize_biom_table import SummarizeBiomTable
> > +      from biom.parse import parse_biom_table
> > +      c = SummarizeBiomTable()
> > +      t = parse_biom_table(open("table.
> biom"))
> > +      result = c(table=t)
> > +      result = c(table=t,qualitative=True)
> > +      result = c(table=t,qualitative=True,input_fp="table.biom")
>
> What about using a modification of option 3 (see my original post above)
> so that the required input table option has an input handler that returns a
> tuple containing the parsed Table and the open filehandle? That way
> --suppress_md5_sum can be respected within the Command, and the Command is
> still filepath-agnostic because it's only operating on a filehandle (which
> could be a list of strings, etc.).
>
> —
> Reply to this email directly or view it on GitHub<https://github.com/biom-format/biom-format/pull/161/files#r5799987>
> .
>