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Allow additional features in medium table definition #39

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jonls opened this issue Sep 16, 2015 · 0 comments
Open

Allow additional features in medium table definition #39

jonls opened this issue Sep 16, 2015 · 0 comments

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@jonls
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jonls commented Sep 16, 2015

It was proposed that additional features should be allowed in the medium table format. Currently the medium table format consists of 4 column (2 required, 2 optional), specifying compound ID, compartment, lower bound and upper bound. With this proposal, additional user defined properties should be allowed after the four existing columns.

The user defined properties should be parsed and be made accessible through the API. For example, with a user defined property "class":

compound        compartment     lower   upper   class
akg     e       0       400     carbon-source
glcD    e       -10     -       carbon-source

This would require that a header be added to the medium table format so that a key can be specified for each property. It would also change the format of the table file to be strictly tab-separated instead of being space-separated as it is now. A new class MediumEntry can be defined so that the additional user defined properties can be held. The properties can be made available from the NativeModel through parse_medium() which would iterate over MediumEntry objects instead of tuples.

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