added a convert.hsa.id.to... (creates a list of ids for each species) and convert.id.list.to.fasta... (formats the id for the blastdbcmd)
cleaned up. also, created a modified version of create.list.of.id.in... that uses the geneID instead
added in the new versions of the cgs creators (dr and ce) that use the geneID. also added the versions needed to create a list of ids in each family
added parse.ci.dr.full.blast... this script uses a blast report to create a cgs for dr and ce.
script works
script now uses tabs instead of spaces
added create.length.proteome.13.08.02.py. this script creates a file with (proteinID) (length)
script works, now calculates the percent coverage by dividing the query length by the allignment length
updated create.coverage.map... with a new way to get percent coverage, updated the tophits format in parse.ci.dr...
script works
archived old scripts, created a new version of all of the coverage mapping scripts (new paths)
script works
changed output to provide the query and the result for the lowest percent coverage
script works, new features
added the new paths into parse.ci.di... and convert.ce/dr. also, added best.hit.spp... (still a work in progress).
updated paths in parse.ci.dr.full.blast.for.cgs... so it works with new files
modified create.length.proteome... so that it gives a better formmatted output, uses the correctly formatted path for the output
fixed a bug where the log output string had the same name as the output
fixed a bug where the wrong thing was printed at the end of the program
updated the filepaths to the .lengths files. still need to add in the ciona and the non-ensembl paths (etc) if this script is to be able to parse the non-ensembl blast report.