Ancestral Reconstruction Pipeline

• Images from hackathon
• 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 < 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>

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>
• -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.>

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