turbomam/seq2ids

Issues

• add cogs to get curations

  #33 opened 2 years ago by turbomam
  1

• db-to-sqlite: sqlite3.OperationalError: table sqlite_master may not be modified

  #31 opened 2 years ago by turbomam
  3

• bash/pgsql2sqlite.sh on Ubuntu 20 complains about [[ operator

  #32 opened 2 years ago by turbomam
  0

• Convert parts_best_match.py into a click CLI application

  #27 opened 2 years ago by sujaypatil96
  0

• Log whole duplicates from the database

  #28 opened 2 years ago by sujaypatil96
  0

• Compute weighted hybrid score for rows in `part_characterization.tsv`

  #29 opened 2 years ago by sujaypatil96
  0

• log the rows from blast and annotation process dropped because of low hybrid score

  #30 opened 2 years ago by sujaypatil96
  0

• double check sql that attempts to triage blast results for uniprot annotation retrieval

  #25 opened 2 years ago by turbomam
  0

• Pick the one best Uniprot BLAST hit for protein coding parts

  #8 opened 2 years ago by turbomam
  3

• related repositories

  #20 opened 2 years ago by turbomam
  2

• add blast db column

  #22 opened 2 years ago by turbomam
  0

• Characterization of some protein-coding modifications might not be specific enough

  #14 opened 2 years ago by turbomam
  1

• Which Uniprot annotations do we want to keep?

  #18 opened 2 years ago by turbomam
  1

• parts table notes

  #19 opened 2 years ago by turbomam
  0

• Postgres structure and notes (initial)

  #7 opened 2 years ago by turbomam
  0

• Are we actually BLASTing against SwissProt or Uniprot?

  #11 opened 2 years ago by turbomam
  0

• Add support for higher organisms

  #17 opened 2 years ago by turbomam
  0

• Add support for characterizing deletions

  #16 opened 2 years ago by turbomam
  0

• resources

  #15 opened 2 years ago by turbomam
  0

• Add support for identifying non-coding modifications

  #13 opened 2 years ago by turbomam
  0

• Determine which columns in the parts table are only filled for STRAINs vs MODIFICATIONs

  #12 opened 2 years ago by turbomam
  0

• Not generally using e-values to filter BLAST hits

  #10 opened 2 years ago by turbomam
  0

• For non-protein-coding parts: identification and annotation similar to Uniprot annotation

  #9 opened 2 years ago by turbomam
  0

• use strict enforcement of column types when creating SQLite tables?

  #6 opened 2 years ago by turbomam
  0

• better requirements documentation required

  #5 opened 2 years ago by turbomam
  0

• inconsistent column typing in SQLite and queries and scripts

  #4 opened 3 years ago by turbomam
  0

• get_uniprot_entries.py: No columns to parse from file, after switching sequence identifier column

  #3 opened 3 years ago by turbomam
  0

• BLAST output doesn't have any unique key in SQLite yet

  #2 opened 3 years ago by turbomam
  0

• changes to blast output (or columns to join)

  #1 opened 3 years ago by turbomam
  0