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BuddySuite V1.3.0
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@biologyguy biologyguy released this 21 Dec 14:59
· 106 commits to master since this release
V1.3.0
a31f138

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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