Available Cross Linking Engines

Kojak

class ursgal.wrappers.kojak_1_5_3.kojak_1_5_3(*args, **kwargs)

Kojak UNode Parameter options at http://www.kojak-ms.org/param/index.html

Reference: Hoopmann MR, Zelter A, Johnson RS, Riffle M, Maccoss MJ, Davis TN, Moritz RL (2015) Kojak: Efficient analysis of chemically cross-linked protein complexes. J Proteome Res 14: 2190-198

Note

Kojak has to be installed manually at the moment! Use folder name: ‘kojak_1_5_3’ in the resources folder.

format_templates()

Returns formatted input files as a dict.

The standard parametern file is used and adjustes.

Returns:keys are the names of the parametern template file
Return type:dict
postflight()

Move the result files to the Kojak folder, since the output files can not be specified manually.

preflight()

Formatting the command line via self.params