Ancestral Reconstruction Pipeline: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
No edit summary |
||
| Line 4: | Line 4: | ||
* [[Images from hackathon]] | * [[Images from hackathon]] | ||
* [[Notes on pipeline details]] | * [[Notes on pipeline details]] | ||
===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 <sub genome 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> | |||
Revision as of 21:18, 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
- -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>