Ancestral Reconstruction Pipeline: Difference between revisions
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*** note: if directory, will batch process all files | *** note: if directory, will batch process all files | ||
* -o <outfile or directory> | * -o <outfile or directory> | ||
====GetContigInput==== | |||
*Remove config file dependency | |||
* -g gid1,gid2,gid3,gid4... <list of common separated coge genome ids> | |||
* -w w1,w2,w3,w4 <list of comma separated weights for genomes -- note these are paired ordered data with the -g option?> | |||
- | |||
Revision as of 21:24, 25 April 2014
Plan for refactoring
GetGenomes: remove config file, add option to specify output dir for output files
- -d<directory of input synmap files>
- -g gid1,gid2,gid3,gid4... <list of common separated coge genome ids>
- -w w1,w2,w3,w4 <list of comma separated syntenic depths for genomes -- note these are paired ordered data with the -g option?>
- -s < subgenome_file>
- -o <output directory for SubGenomeInGeneOrder OrthologSets GenomeInString files>
MWMPython: http://jorisvr.nl/maximummatching.html needs command line options for
- -i <input file or directory>
- File type is a set of vertex vertex weight
- note: if directory, will batch process all files
- -o <outfile or directory>
GetContigInput
- Remove config file dependency
- -g gid1,gid2,gid3,gid4... <list of common separated coge genome ids>
- -w w1,w2,w3,w4 <list of comma separated weights for genomes -- note these are paired ordered data with the -g option?>
-