Robaina/Pynteny

Issues

• Download and prepare PFAM-A database

  #71 opened 10 months ago by Robaina
  1

• Merge PGAP and PFAM meta info into a single file

  #94 opened a year ago by Robaina
  0

• No output from example API

  #91 opened a year ago by wchow
  2

• Enable selection of maximum processes in pynteny search (hmmer)

  #89 opened 2 years ago by Robaina
  1

• Report of pynteny build running out of memory in a very large database

  #80 opened 2 years ago by Robaina
  1

• Report of multi-threading in pynteny build not working

  #79 opened 2 years ago by Robaina
  0

• File manager not showing up correctly in Firefox

  #17 opened 2 years ago by Robaina
  1

• Double check peptide labels in database

  #27 opened 2 years ago by Robaina
  0

• Update pynteny in bioconda and check installation

  #76 opened 2 years ago by Robaina
  0

• requests + tqdm instead of python-wget

  #83 opened 2 years ago by Robaina
  0

• Upload Streamlit-Aggrid to bioconda or remove dependency

  #77 opened 2 years ago by Robaina
  0

• Check HMM name retrieval from synteny structura

  #78 opened 2 years ago by Robaina
  0

• Optional prepend file name when multiple input files

  #74 opened 2 years ago by Robaina
  0

• Update docs

  #65 opened 2 years ago by Robaina
  0

• Implement database build from already generated peptide database

  #66 opened 2 years ago by Robaina
  1

• Download PFAM database and split models into separate files

  #69 opened 2 years ago by Robaina
  1

• Enable usage of file name as genome ID in pynteny build

  #67 opened 2 years ago by Robaina
  0

• Deal with genome ID when building peptide database from genbank files

  #29 opened 2 years ago by Robaina
  1

• Add minimal graphical example of a syntenic block

  #61 opened 2 years ago by Robaina
  1

• Ensure file inputs are objects of class Path

  #41 opened 2 years ago by Robaina
  0

• PyOpenSic: Some more minor changes

  #59 opened 2 years ago by Robaina
  0

• Removing config file upon package uninstall

  #55 opened 2 years ago by Robaina
  0

• Remove default install dir of PGAP database, make --outdir param required in pynteny download

  #56 opened 2 years ago by Robaina
  0

• PyOpenSci REVIEW: pynteny.download and config default paths

  #49 opened 2 years ago by Robaina
  0

• Making Pynteny pip-installable

  #24 opened 2 years ago by Robaina
  1

• Change repo structure to avoid issues with testing

  #53 opened 2 years ago by Robaina
  0

• PyOpenSci - REVIEW: enhance documentation and contributing.md

  #48 opened 2 years ago by Robaina
  0

• PyOpenSci REVIEW - Static classes

  #44 opened 2 years ago by Robaina
  0

• PyOpenSci REVIEW - Minor changes

  #42 opened 2 years ago by Robaina
  0

• PyOpenSci REVIEW - Extract / Refactor nested functions

  #46 opened 2 years ago by Robaina
  0

• Refactor code to meet PEP8

  #39 opened 2 years ago by Robaina
  0

• GitHub Action "test" suddenly failing for linux

  #38 opened 2 years ago by Robaina
  1

• Build.getTestDataPath() no longer works after relocating tests outside package

  #37 opened 2 years ago by Robaina
  1

• Python version lower than 3.10?

  #32 opened 2 years ago by Robaina
  0

• Create a devcontainer for codespaces?

  #33 opened 2 years ago by Robaina
  2

• Add codecov to github action

  #35 opened 2 years ago by Robaina
  1

• Add option to match hmm hits on the same strand only (either one of the two)

  #11 opened 2 years ago by Robaina
  1

• Prepare GitHub Action for CI

  #31 opened 2 years ago by Robaina
  1

• Check docstrings

  #25 opened 2 years ago by Robaina
  1

• Change docstring format to Google format

  #28 opened 2 years ago by Robaina
  0

• Add code snippets from examples in README.md

  #26 opened 2 years ago by Robaina
  0

• Restructure Project

  #22 opened 2 years ago by Robaina
  0

• Create online documentation

  #23 opened 2 years ago by Robaina
  1

• Incomplete documentation for --unordered

  #20 opened 2 years ago by Robaina
  1

• Pynteny search results table: sorting when "--unordered"

  #21 opened 2 years ago by Robaina
  3

• Add search optional parameter to reuse hmmer search result tables

  #18 opened 2 years ago by Robaina
  0

• Include prodigal translation in Database object

  #14 opened 2 years ago by Robaina
  1

• Remove missing (from PGAP directory) entries from PGAP meta data upon donwload

  #13 opened 2 years ago by Robaina
  1

• Save log to text file

  #12 opened 2 years ago by Robaina
  1

• Deal with cases where hmms in hmm groups don't map to the same sequences

  #9 opened 2 years ago by Robaina
  1