General
- Bring entire suite up to >95% unit test coverage
- Track coverage with Coveralls
- Use fixtures in unit test suite
- Start monitoring the repository on Travis-CI
- Switch to setuptools installation and PyPI distribution
- Include a final (optional) setup script in BuddySuite.py to configure caching and config.ini
- Move all MyFuncs.py functions to buddy_resources.py
- Remove the '-p' flag from all modules
- Overhaul of usage and crash traceback reporting
- Full support for Windows
- Support for earlier versions of Python (at least 3.3)
- All hash_ids functions now accept seed values for reproducibility
- Some performance upgrades by building fewer long strings with +=
- On crash, check database of errors and report upgrades to user
- Include files size stats in usage reports
- Move all module specific _stderr() and _stdout functions to buddy_resources.py
- Graceful handling of malformed user input in many functions
- Dozens of bug fixes
SeqBuddy
New functions
- transmembrane_domains()
- Calls the TopCons servers and processes all returned files
- SeqBuddy.print_hashmap()
- SeqBuddy.reverse_hashmap()
- prosite_scan()
- Calls the prosite scan server and process all returned files
- extract_feature_sequences()
Upgrades
- Add 'ambiguous' functionality to find_patterns()
- Allow pull_records() to read from a file
- Support reading of SwissProt format
- degenerate_sequence() provides list of tables when no argument passed in
- Complete re-write of find_orf()
AlignBuddy
New functions
- AlignBuddy.append_pos_map
Upgrades
- Smarter handling of third-party MSA programs
- generate_tree now accommodates multiple alignments
PhyloBuddy
New functions
- collapse_polytomies()
- clean_newick()
Upgrades
- Smarter handling of third-party phylo inference programs
- Support for RAxML bootstrap replicates
DatabaseBuddy
Upgrades
- Major overhaul throughout the program. Much more stable now.
- Better use of color in live shell