Ancestral Reconstruction Pipeline: Difference between revisions
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[[Image:20140424 165903.jpg|thumb|left|400px | [[Image:20140424 165903.jpg|thumb|left|400px]] [[Image:Photo.JPG|thumb|left|400px]] | ||
[[Image:Photo.JPG|thumb|left|400px | |||
* [[Images from hackathon]] | *[[Images from hackathon]] | ||
* [[Notes on pipeline details]] | *[[Notes on pipeline details]] | ||
===Plan for refactoring=== | === Plan for refactoring === | ||
* GetGenomes: | |||
** -d | * GetGenomes: remove config file, add option to specify output dir for output files | ||
** -g gid1,gid2,gid3,gid4... | ** -d<directory of input synmap files> | ||
** -w w1,w2,w3,w4 | ** -g gid1,gid2,gid3,gid4... <list of common separated coge genome ids> | ||
** -s <sub | ** -w w1,w2,w3,w4 <list of comma separated syntenic depths for genomes -- note these are paired ordered data with the -g option?> | ||
** -o | ** -s <sub></sub> | ||
* MWMPython: http://jorisvr.nl/maximummatching.html needs command line options for | ** -o <output directory for SubGenomeInGeneOrder OrthologSets GenomeInString files> | ||
** -i | *MWMPython: http://jorisvr.nl/maximummatching.html needs command line options for | ||
*** File type is a set of vertex vertex weight | ** -i <input file or directory> | ||
*** File type is a set of vertex vertex weight | |||
*** note: if directory, will batch process all files | *** note: if directory, will batch process all files | ||
** -o | ** -o <outfile or directory> | ||
Revision as of 21:20, 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>