Need to develop the menus for relocate3.py to run the steps. Reminder the goal is to run the mapping/aln step of each strain/individual as a separate independent job, produce summary results (BAM?, BED?) files of the reads which contain TEs and their locations in the reference genome.
Proposed menu function names could be
- process_individual -- eg map reads for an individual to a genome (1-N seq libraries)
- gather_mapped_individual -- eg gather the mapped read locations to score the TE
- statistics
- classify -- eg classify reference and non-reference insertions, homozygous/heterozygous
Need to develop the menus for relocate3.py to run the steps. Reminder the goal is to run the mapping/aln step of each strain/individual as a separate independent job, produce summary results (BAM?, BED?) files of the reads which contain TEs and their locations in the reference genome.
Proposed menu function names could be