Other Functions

The FAS package contains a number of additional functions that are not part of the main calculation. Use the -h option to get more information on each of them.

fas.calcComplexity

This function allows you to calculate the complexity of the overlap graphs, the number of alternative overlap free paths, for a set of proteins.

fas.getDomains

This function creates .domain files as input for PhyloProfile without calculating the FAS score.

fas.splitJson

Allows to extract a subset of protein architectures from an annotation .json file into a separate file.

fas.checkAnno

Checks annotation .json file of a multifasta file for missing proteins.

fas.getProtByAnno

Find proteins in a .json file that contain a certain feature/domain.

fas.overlapStatistics

Get an overview of the overlaps between two feature classes in a given annotation file. This should give an idea if it would make to merge two classes into one for linearization.

fas.runFdogFas

This function is specifically used in fDOG. It is dependent on the file and folder formatting of fDOG to produce the final PhyloProfile output of the pipline.