BuddySuite V1.2.0

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