Ancestral Reconstruction Pipeline: Difference between revisions
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*[[Images from hackathon]] | *[[Images from hackathon]] | ||
*[[Notes on pipeline details]] | *[[Notes on pipeline details]] | ||
=== Plan for refactoring === | === 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> | ** -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?> | ** -w w1,w2,w3,w4 <list of comma separated syntenic depths for genomes -- note these are paired ordered data with the -g option?> | ||
Revision as of 21:21, 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>
- -i <input file or directory>