Ancestral Reconstruction Pipeline: Difference between revisions

Revision as of 21:52, 25 April 2014

-d<directory of input synmap files>
-g gid1,gid2,gid3,gid4... <list of common separated coge genome ids>
-p p1,p2,p3,p4 <list of comma separated ploidy levels for genomes -- note these are paired ordered data with the -g option?>
-s < subgenome_file>
-o <output directory for SubGenomeInGeneOrder OrthologSets GenomeInString files>

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?>
-wa <threshold minimum adjacency score for keeping a contig. Called 'weightOfAdjacent' in original config file>
-i <input file: GenomesInString from program GetGenomes>

Note: Output is now a tab delimited file with each line containing: vertex vertex weight . These data will be used by the MEMPython data below

-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> If no option is specified, the results go to STDOUT

Note: goal is to get everything onto the command line. Currently, several of the files are hardcoded

-cl <threshold minimum contig length. Called 'minimumGeneGroupLength' in original config file>
-b <Number of bins for assignment to ancestral chromosomes. Called 'AncChrNumber' in original config file> (Note: this may be removed if this info can be derived from the input -- specifically the SubGenomesInGeneOrder file).)

Note: genomeInContigIndex is specified in the config file. This is the weighting for each subgenome. Need to discuss how best to deal with these.

@@ Line 9: / Line 9: @@
 * -d&lt;directory of input synmap files&gt;
 * -g gid1,gid2,gid3,gid4... &lt;list of common separated coge genome ids&gt;
-* -w w1,w2,w3,w4 &lt;list of comma separated syntenic depths for genomes -- note these are paired ordered data with the -g option?&gt;
+* -p p1,p2,p3,p4 &lt;list of comma separated ploidy levels for genomes -- note these are paired ordered data with the -g option?&gt;
 * -s < subgenome_file>
 * -o &lt;output directory for SubGenomeInGeneOrder OrthologSets GenomeInString files&gt;