biocore/microprot

Issues

• keep output files in ffindex format

  #62 opened 7 years ago by tkosciol
  2

• refactor the Snakemake pipeline

  #76 opened 5 years ago by tkosciol
  0

• Snakemake: secondary predictions

  #60 opened 5 years ago by tkosciol
  1

• Uniclust and Uniboost performance on contact predictions

  #24 opened 5 years ago by tkosciol
  3

• pipeline: use DHM to keep databases in memory

  #61 opened 7 years ago by tkosciol
  1

• BUG: `MSA_ripe` rule fails on some non-standard amino acids

  #75 opened 7 years ago by tkosciol
  0

• auto build and update microprot_db and HH-suite compatible DB

  #63 opened 7 years ago by tkosciol
  0

• feature request: `split_search` by % identities

  #72 opened 5 years ago by tkosciol
  3

• BUG: `split_search` does not split correctly in some cases

  #71 opened 7 years ago by tkosciol
  4

• some records do not get propagated from log to `microprot_db`

  #70 opened 7 years ago by tkosciol
  0

• refactor setup.py and repo structure

  #69 opened 7 years ago by tkosciol
  0

• unit tests for `snakemake_helpers`

  #68 opened 7 years ago by tkosciol
  0

• Snakemake: reorganize output structure

  #52 opened 7 years ago by tkosciol
  0

• Read MSA size & data source for `append_db` function in Snakemake

  #48 opened 7 years ago by tkosciol
  1

• calculate effective family size for MSA_ripe rule

  #26 opened 8 years ago by tkosciol
  11

• add match identifier to `match` files

  #65 opened 7 years ago by tkosciol
  3

• BUG: split_search.mask_sequence does not pick optimal fragments

  #51 opened 7 years ago by tkosciol
  3

• Snakemake: code outside of rules executed multiple times

  #58 opened 7 years ago by tkosciol
  0

• snakemake: edge cases and extensions

  #29 opened 7 years ago by tkosciol
  1

• index DB: append

  #22 opened 7 years ago by tkosciol
  0

• Snakemake scaffold

  #5 opened 7 years ago by tkosciol
  0

• Snakemake: auto-generate benchmarking and reporting info

  #57 opened 7 years ago by tkosciol
  0

• BUG: split_sequence error, possible HHsearch issue

  #55 opened 7 years ago by tkosciol
  2

• cluster Micronota genes: extract representative sequences from clustering

  #30 opened 7 years ago by tkosciol
  1

• cluster Micronota genes

  #21 opened 7 years ago by tkosciol
  3

• BUG: calculate_Neff fails if 1 sequence in output

  #49 opened 7 years ago by tkosciol
  1

• BUG: calculate_Neff crashes if duplicate entries in DissimilarityMatrix

  #53 opened 7 years ago by tkosciol
  4

• IMPROVEMENT: split_search should modify output name, if residue numbers in name

  #43 opened 7 years ago by tkosciol
  2

• BUG: split_search skips non_match sequences if --frag-len too large

  #42 opened 7 years ago by tkosciol
  9

• BUG: process_fasta.extract_sequences cannot handle lists of int

  #39 opened 7 years ago by tkosciol
  0

• REQUEST: process_fasta.extract_sequences should be able to read sequence ranges

  #40 opened 7 years ago by tkosciol
  0

• IMPROVEMENT: split_sequence naming

  #34 opened 7 years ago by tkosciol
  1

• IMPROVEMENT: split_sequence non_match fragment length

  #35 opened 7 years ago by tkosciol
  3

• BUG: split_search parsing HHsearch output

  #33 opened 7 years ago by tkosciol
  4

• index DB: search

  #23 opened 8 years ago by tkosciol
  1

• split sequence

  #4 opened 8 years ago by tkosciol
  8

• MMSeqs2 install

  #28 opened 8 years ago by tkosciol
  1

• domain split: parser

  #7 opened 8 years ago by tkosciol
  1

• secondary structure and disorder predictions

  #8 opened 8 years ago by tkosciol
  16

• MSA: decision

  #10 opened 8 years ago by tkosciol
  1

• MSA: generate

  #9 opened 8 years ago by tkosciol
  1

• domain split: optimize

  #6 opened 8 years ago by tkosciol
  1

• PDB match: search

  #2 opened 8 years ago by tkosciol
  1

• pre-processing script: generate PDB100

  #12 opened 8 years ago by tkosciol
  3

• pre-processing: extract gene from genome

  #11 opened 8 years ago by tkosciol
  3

• PDB match: parser

  #3 opened 8 years ago by tkosciol
  7

• Python version

  #14 opened 8 years ago by sjanssen2
  2

• Travis

  #15 opened 8 years ago by sjanssen2
  1