chmod +x *.py
Mod variable 'Usage' to 'usage' for subsequent call in stitch_six_frame_stops.
Add vim plugin folder to .gitignore
Add prodigalout file check for new version's closer match to GenBank format.
Updated spacing, trailing whitespace, etc for PyLint. Added pylint files with remaining suggestions.
Added --debug flag for more (code debug help) output.
Added function print_debug; changed if debug lines to use that function.
Refactor: new seqrecord_parse function to get features; eliminate SeqIO as prodigal's output does not match.
Refactor: add functions print_verbose, print_verbose_list to replace 'if verbose' sections for simplicity.
Create folders for easier perusal to end users. Keep main script in main dir.
Add log_debug function, add to each clines.append.
Mod clines.append, use str() to concat with log_debug.
Add command line params: keep_logs, log_dir; mod log_debug to log_output.
Add TODO: allow option file for cmdline args
Logs: repaired outstream handle.
corrected typo: variable 'usage' should be 'Usage'
Added citation information as well as dependency versions required to run the pipeline
Within the function 'build_blast_input': 'primer.forward.seq' and 'primer.reverse.seq' were updated to 'primer.forward_seq' 'primer.reverse_seq' respectively
updated / reworded section text
added basic use information