biologyguy/BuddySuite

Issues

• "FTP Error: got more than 8192 bytes"

  #127 opened 3 years ago by dougwyu
  1

• Error on Anaconda Environment Install: ModuleNotFoundError: No module named 'buddy_resources'

  #128 opened 3 years ago by john-k-boyd
  5

• 'Lazy' imports.

  #92 opened 8 years ago by biologyguy
  1

• AlignBuddy in multiple cores

  #126 opened 7 years ago by amartinezgarcia
  5

• Error report: DBBuddy

  #125 opened 7 years ago by biologyguy
  0

• Format wiki pages for extended command line help

  #87 opened 8 years ago by biologyguy
  2

• Sb.split_to_x_files() and Sb.split_to_x_records()

  #119 opened 7 years ago by biologyguy
  1

• Pull Records blank line issue

  #124 opened 7 years ago by biologyguy
  0

• NEXUS interleaved/sequential

  #100 opened 7 years ago by biologyguy
  3

• Return no records when using Sb.pull_recs() with empty file

  #120 opened 7 years ago by biologyguy
  0

• Add support for circular sequences

  #109 opened 7 years ago by biologyguy
  1

• DatabaseBuddy save states across Python versions

  #107 opened 7 years ago by biologyguy
  1

• Alb.validate_alignments()

  #116 opened 7 years ago by biologyguy
  0

• Sb.accn2name()

  #117 opened 7 years ago by biologyguy
  0

• Function requests

  #90 opened 7 years ago by biologyguy
  1

• Allow DatabaseBuddy to run without launching a live shell

  #104 opened 7 years ago by biologyguy
  1

• Dynamically adjust argparse help output to fit the user's terminal window.

  #93 opened 7 years ago by biologyguy
  1

• Start-end coordinates for `find` tools

  #98 opened 7 years ago by biologyguy
  1

• Add a provenance tracker

  #103 opened 8 years ago by biologyguy
  0

• Create Jupyter notebooks to demonstrate functionality

  #85 opened 8 years ago by biologyguy
  0

• Wrap alignment and tree inference web services

  #99 opened 8 years ago by biologyguy
  0

• Catch multiple flags

  #102 opened 8 years ago by biologyguy
  0

• DBBuddy result slices

  #101 opened 7 years ago by biologyguy
  1

• DBBuddy summaries

  #97 opened 7 years ago by biologyguy
  1

• Implement -s flag to set a seed value.

  #91 opened 7 years ago by biologyguy
  1

• Test builds on various Python versions with Tox

  #96 opened 7 years ago by biologyguy
  1

• Python 3.6 breaks Travis-CI builds

  #106 opened 7 years ago by biologyguy
  1

• seqbuddy rename ids

  #83 opened 8 years ago by sellisd
  4

• problem with deleting invariant sites

  #114 opened 7 years ago by thkuo
  1

• Try to manage input as streams instead of storing everything in RAM

  #94 opened 8 years ago by biologyguy
  2

• NCBI switched to full ACCN support (drops GI)

  #111 opened 8 years ago by biologyguy
  1

• Prune taxa error

  #110 opened 8 years ago by biologyguy
  4

• Properly handle KeyboardInterrupt in DBBuddy

  #89 opened 8 years ago by biologyguy
  0

• Feature requests for V 1.3

  #68 opened 8 years ago by biologyguy
  0

• Add gff3 support

  #95 opened 8 years ago by biologyguy
  0

• Consider migrating Wiki to PanDocs

  #81 opened 8 years ago by biologyguy
  0

• PhyloBuddy handling of unrecognized args

  #88 opened 8 years ago by biologyguy
  1

• Create 'TimeIt' program to performance test all BuddySuite tools

  #76 opened 8 years ago by biologyguy
  0

• Switch README to rst format

  #82 opened 8 years ago by biologyguy
  1

• combining seqbuddy -dm and -cs command line options

  #84 opened 8 years ago by sellisd
  1

• Wiki page for extract_feature_sequences

  #79 opened 8 years ago by biologyguy
  2

• Feature: SeqBuddy.pull_recs_with_feature

  #80 opened 8 years ago by biologyguy
  1

• Write unit tests for buddy_resources

  #70 opened 8 years ago by biologyguy
  1

• Handle the common raxml names (PhyloBuddy)

  #77 opened 8 years ago by biologyguy
  1

• replacements function in buddy_resources does weird things with parenthesis (when searching from right to left)

  #78 opened 8 years ago by KarlKeat
  1

• Create dedicated folder for diagnostics

  #69 opened 8 years ago by KarlKeat
  1

• Weird Imports

  #65 opened 8 years ago by Cabalist
  2

• SB prosite_scan and cd_hit functions break alphabetic order

  #64 opened 8 years ago by KarlKeat
  2

• Unknown Blast binaries and zips in codebase

  #66 opened 8 years ago by Cabalist
  2

• Link to MEME suite in SB Purge page is dead

  #67 opened 8 years ago by KarlKeat
  4