weiju/cmonkey-python — pull request #34 by sdanzige (2014-10-08 22:32:49+00:00)
Title: Run human 'out of the box'.

This is the first version that includes the ability to run human 'out of the box'. It does this by storing a sample interaction file in the example_data, and by significant changes to the rsat code to allow cMonkey to download gene and sequence data.

These changes to RSAT include the ability to specify from the command line a custom RSAT URL and a custom RSAT feature name (e.g.) protein_coding instead of features.

NOTE: This version has not been tested on organisms other than human.
NOTE: This version does not parse the command line parameters for the two new flags in the same manner as the other ones. This should be fixed so that the default value is 'None' which forces them to be read from an .ini file

Future updates should include:
1) Code to parse Biogrid instead of String and automatically select the correct organism data. Note: biogrid uses NCBI taxonomy ids, for this human is 9606. These taxonomy IDs can be found in RSAT in the organism.tab file.

2) Automatic detection so that once the organism is specified as HSA, all of the other parameters (such as the correct RSAT database and protein interaction file) are automatically set to working values.