#object-files:
pybin/Cosmic/TSV.py
pybin/Cosmic/VCF.py
pybin/TCGA/MAFcounters.py
pybin/TCGA/MAF.py
pybin/TCGA/MAFSampleCountsList.py
#functional script files:
##used for name fixes:
check_against_lengths_file.py
exon_sizer.py
MAF_collect_unique_entrez_ids.py
MAF_collect_unique_sumbols.py
parse_symbolcheck_output.py
update_names_entrez.py
##used for counting and grouping (splitting file by size boundaries):
maf_counter.py
split_maf_with_counts.py
This is a work in progress. Hope to eventually combine these diverse functions into a single command-driven script.
#Current Tasks:
- Complete unified name-fixing script
- Unify all scripts into a single command-driven script
- switch from argparse module to Click module