usage: prok_tuxedo.py [-h] -g G [-L L] [-p P] [-o O] readfiles [readfiles ...]

positional arguments: readfiles whitespace sep list of read files. shoudld be in corresponding order as library list. ws separates libraries, a comma separates replicates, and a percent separates pairs.

optional arguments: -h, --help show this help message and exit -g G csv list of directories each containing a genome file *.fna and annotation *.gff -L L csv list of library names for comparison -p P JSON formatted parameter list for tuxedo suite keyed to program -o O output directory. defaults to current directory.

An example run (small pair against itself):

python ./prok_tuxedo.py -L lib1,lib2 -g /home/anwarren/mcclelland/reference/14028s_test /home/anwarren/mcclelland/test/READ1_SHORT.fastq%/home/anwarren/mcclelland/test/READ2_SHORT.fastq /home/anwarren/mcclelland/test/READ1_SHORT.fastq%/home/anwarren/mcclelland/test/READ2_SHORT.fastq