Ancestral Reconstruction Pipeline
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>
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?>
- -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
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> If no option is specified, the results go to STDOUT
GetContigOutputAndScaffoldInput
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.
- -co <configoutput file generated by the MWMPython program>