Releases
V1.3.0
General
Performance scanning module developed (with thanks to Sofia Barreira @alicarea )
Implement --random_seed flag across the suite, allowing random components to become reproducible
Implement --restrict flag across the suite, allowing a function to be run on only a subset of records
buddy_resources.RunTime() upgraded
Fix several GenBank format annotation bugs
Handle unknown flags more gracefully and informatively
Better handling of error messages when piping output from one Buddy module to another
Completely remove the ETE3 dependency (which also removes PyQt4)
Letter annotations no longer cause everything to break
clean_regex() function added to buddy_resources, which checks that a user supplied regex is valid
Many unit-test updates to account for some changes in output caused by BioPython 1.69
TempDir() given a new copy_to() method
In conjunction with upcoming changes to BioPython, allow output in NEXUS-interleaved and NEXUS-sequential
SeqBuddy
New functions
max_records()
min_reocrds()
in_silico_digest() (with thanks to Paul Gonzalez @paulgzlz )
keep_taxa()
delete_taxa()
prepend_organism()
delete_recs_with_feature()
taxonomic_breakdown()
order_recs_by_len()
amend_metadata()
split_by_seq_number() (with thanks to Paul Gonzalez @paulgzlz )
split_by_file_number() (with thanks to Paul Gonzalez @paulgzlz )
Upgrades
Switch annotate() function default output to GenBank
Implement feature ranges in extract_feature_sequences
find_orfs() given new parameters min_size
and rev_comp
, and matches now numbered from large to small
pull_recs() allows searching in the description now
delete_records() allows searching in the description now
find_restriction_sites now handles RNA sequences and circular sequences (with thanks to Paul Gonzalez @paulgzlz )
Various bug fixes in BLAST-related functions, increasing stability
find_pattern() now returns start-end coords
AlignBuddy
New functions
faux_alignment()
Create a meaningless alignment from a collection of sequences
extract_feature_sequences()
percent_id()
delete_invariant_sites
generate_hmm()
position_frequency_matrix()
Upgrades
Update extract_regions() syntax to match that of SeqBuddy
New align_tool attribute added to AlignBuddy objects
Move MSA alias detection into buddy_resources
Add 'weighted' parameter to consensus_sequence() (with thanks to Paul Gonzalez @paulgzlz )
PhyloBuddy
New functions
Upgrades
display_trees() function now sends output to the default web browser as SVG, instead of PyQt
RAxML -x flag now handled for rapid bootstrapping
DatabaseBuddy
Upgrades
Remove all reference to GI numbers to comply with NCBI phasing them out. Everything is accession numbers now.
Much better handling of KeyboardInterrupt. It now behaves more like you would expect from a shell environment (instead of crashing out...)
Allow larger files to be downloaded from NCBI, using the rettype 'gbwithparts'
Allow slices of results to be displayed with show
Can now run without launching a live shell (do a search and return the results from bash)
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