General
- Update error reporting to include more function information
- Timeout usage upload and error report to prevent hangs when not connected to internet
- Catch Python2 and exit gracefully
- Add self.hash_map attributes to core Buddy classes
SeqBuddy
Upgrades
- Allow blast() function to query another sequence file instead of depending on a pre-made blast database
- Allow additional BLAST parameters to be passed in by the user
- Accept a separator character argument in make_ids_unique()
- Clean up rename() so to old ids are stored in the record description. Most output formats do not print this information, which significantly cleans up the retuned records.
- Make order_ids() numeric aware. i.e., return ['gene1', 'gene4', 'gene9', 'gene12', 'gene101'] instead of ['gene1', 'gene101', 'gene12', 'gene4', 'gene9'].
- Re-name extract_range() to extract_regions() and completely rewrite to allow a more flexible selection of which residues to return.
- New internal methods for re-mapping features to sequences that have been truncated in some way
AlignBuddy
New functions
- hash_ids
- bootstrap
Upgrades
- Un-hash all temporary files after generating an MSA if those files are being kept
- Add AlignBuddy lengths() method and modify the write() method to accept an out_format
- New internal methods for re-mapping features to alignments that have been truncated in some way
- Numeric-aware order_ids()
- Re-name extract_range() to extract_regions()
PhyloBuddy
Upgrades
- root() function now accepts regular expressions
- Hash sequence ids before running 3rd party tree building programs, then remap ids afterwards. This allows the user to name their sequences whatever they like without worry that the other software will break or rename their records.
- Add 'quiet' support to generate_tree()