Robaina/Pynteny issues and pull requests

#94 - Merge PGAP and PFAM meta info into a single file

Issue - State: open - Opened by Robaina about 1 year ago
Labels: enhancement

#93 - Robaina/issue71

Pull Request - State: closed - Opened by Robaina about 1 year ago - 1 comment

#92 - No output from example API

Pull Request - State: closed - Opened by Robaina about 1 year ago - 1 comment

#91 - No output from example API

Issue - State: closed - Opened by wchow about 1 year ago - 2 comments
Labels: bug

#90 - changed processes command

Pull Request - State: closed - Opened by Robaina over 1 year ago - 1 comment
Labels: enhancement

#89 - Enable selection of maximum processes in pynteny search (hmmer)

Issue - State: closed - Opened by Robaina over 1 year ago - 1 comment
Labels: enhancement

#88 - 80 report of pynteny build running out of memory in a very large database

Pull Request - State: closed - Opened by Robaina over 1 year ago
Labels: enhancement

#87 - include processes parameter in pynteny build

Pull Request - State: closed - Opened by Robaina over 1 year ago - 2 comments
Labels: refactor

#86 - test bioconda build on macos and ubuntu

Pull Request - State: closed - Opened by Robaina over 1 year ago - 1 comment

#84 - Requests + tqdm instead of python-wget

Pull Request - State: closed - Opened by Robaina over 1 year ago - 1 comment

#83 - requests + tqdm instead of python-wget

Issue - State: closed - Opened by Robaina over 1 year ago
Labels: enhancement

#81 - 77 Remove Streamlit App

Pull Request - State: closed - Opened by Robaina over 1 year ago - 1 comment

#80 - Report of pynteny build running out of memory in a very large database

Issue - State: closed - Opened by Robaina over 1 year ago - 1 comment
Labels: enhancement

#79 - Report of multi-threading in pynteny build not working

Issue - State: closed - Opened by Robaina over 1 year ago
Labels: bug

#78 - Check HMM name retrieval from synteny structura

Issue - State: closed - Opened by Robaina over 1 year ago
Labels: enhancement

#77 - Upload Streamlit-Aggrid to bioconda or remove dependency

Issue - State: closed - Opened by Robaina over 1 year ago
Labels: code review

#76 - Update pynteny in bioconda and check installation

Issue - State: closed - Opened by Robaina over 1 year ago
Labels: code review

#75 - 74 optional prepend file name when multiple input files

Pull Request - State: closed - Opened by Robaina almost 2 years ago - 1 comment

#74 - Optional prepend file name when multiple input files

Issue - State: closed - Opened by Robaina almost 2 years ago

#73 - Adjacent repeated genes

Pull Request - State: closed - Opened by Robaina almost 2 years ago
Labels: bug

#72 - update docs

Pull Request - State: closed - Opened by Robaina almost 2 years ago - 1 comment

#71 - Download and prepare PFAM-A database

Issue - State: closed - Opened by Robaina almost 2 years ago - 1 comment
Labels: enhancement, good first issue

#70 - 69 download pfam database and split models into separate files

Pull Request - State: closed - Opened by Robaina almost 2 years ago - 1 comment

#69 - Download PFAM database and split models into separate files

Issue - State: closed - Opened by Robaina almost 2 years ago - 1 comment
Labels: enhancement

#68 - add file name to files in fasta dir

Pull Request - State: closed - Opened by Robaina almost 2 years ago - 1 comment

#67 - Enable usage of file name as genome ID in pynteny build

Issue - State: closed - Opened by Robaina almost 2 years ago
Labels: enhancement

#66 - Implement database build from already generated peptide database

Issue - State: closed - Opened by Robaina almost 2 years ago - 1 comment
Labels: enhancement

#65 - Update docs

Issue - State: closed - Opened by Robaina almost 2 years ago
Labels: documentation

#64 - 29 deal with genome id when building peptide database

Pull Request - State: closed - Opened by Robaina almost 2 years ago - 1 comment

#63 - Ensure file inputs are of type Path

Pull Request - State: closed - Opened by Robaina almost 2 years ago - 1 comment
Labels: enhancement, refactor

#62 - Chore/add qoc config

Pull Request - State: closed - Opened by Batalex almost 2 years ago - 3 comments

#61 - Add minimal graphical example of a syntenic block

Issue - State: closed - Opened by Robaina almost 2 years ago - 1 comment
Labels: documentation, enhancement

#60 - PyOpenSci REVIEW - 59 some more minor changes

Pull Request - State: closed - Opened by Robaina almost 2 years ago - 1 comment
Labels: refactor, code review

#59 - PyOpenSic: Some more minor changes

Issue - State: closed - Opened by Robaina almost 2 years ago
Labels: enhancement, code review

#58 - added config to install dir

Pull Request - State: closed - Opened by Robaina almost 2 years ago - 1 comment
Labels: enhancement, code review

#57 - PyOpenSci REVIEW - remove default location for PGAP download

Pull Request - State: closed - Opened by Robaina almost 2 years ago - 1 comment
Labels: enhancement, refactor, code review

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

Issue - State: closed - Opened by Robaina almost 2 years ago
Labels: enhancement

#55 - Removing config file upon package uninstall

Issue - State: closed - Opened by Robaina almost 2 years ago
Labels: enhancement

#54 - change structure to adopt /src layout

Pull Request - State: closed - Opened by Robaina almost 2 years ago - 1 comment
Labels: enhancement, refactor

#53 - Change repo structure to avoid issues with testing

Issue - State: closed - Opened by Robaina almost 2 years ago
Labels: enhancement, refactor

#52 - 49-pyopensci-review-pyntenydownload-and-config-default-paths

Pull Request - State: closed - Opened by Robaina almost 2 years ago

#51 - PyOpenSci REVIEW - config and download default directories

Pull Request - State: closed - Opened by Robaina almost 2 years ago - 9 comments
Labels: enhancement, code review

#50 - PyOpenSci REVIEW - add setup to docs, add building docs to contributing

Pull Request - State: closed - Opened by Robaina almost 2 years ago - 1 comment
Labels: enhancement, code review

#49 - PyOpenSci REVIEW: pynteny.download and config default paths

Issue - State: closed - Opened by Robaina almost 2 years ago
Labels: enhancement, code review

#48 - PyOpenSci - REVIEW: enhance documentation and contributing.md

Issue - State: closed - Opened by Robaina almost 2 years ago
Labels: enhancement, code review

#47 - PyOpenSci REVIEW - extract nested functions in LabelledFASTA

Pull Request - State: closed - Opened by Robaina almost 2 years ago - 1 comment
Labels: refactor, code review

#46 - PyOpenSci REVIEW - Extract / Refactor nested functions

Issue - State: closed - Opened by Robaina almost 2 years ago
Labels: refactor, code review

#45 - PyOpenSci REVIEW - extract static classes and transfer to own modules

Pull Request - State: closed - Opened by Robaina almost 2 years ago - 1 comment
Labels: refactor, code review

#44 - PyOpenSci REVIEW - Static classes

Issue - State: closed - Opened by Robaina almost 2 years ago
Labels: refactor

#43 - PyOpenSci REVIEW - minor updates

Pull Request - State: closed - Opened by Robaina almost 2 years ago - 3 comments
Labels: refactor, code review

#42 - PyOpenSci REVIEW - Minor changes

Issue - State: closed - Opened by Robaina almost 2 years ago
Labels: enhancement, refactor

#41 - Ensure file inputs are objects of class Path

Issue - State: closed - Opened by Robaina almost 2 years ago
Labels: enhancement

#40 - PyOpenSci REVIEW - Refactor code to meet PEP8

Pull Request - State: closed - Opened by Robaina almost 2 years ago - 1 comment
Labels: refactor

#39 - Refactor code to meet PEP8

Issue - State: closed - Opened by Robaina almost 2 years ago
Labels: refactor

#38 - GitHub Action "test" suddenly failing for linux

Issue - State: closed - Opened by Robaina almost 2 years ago - 1 comment
Labels: bug

#37 - Build.getTestDataPath() no longer works after relocating tests outside package

Issue - State: closed - Opened by Robaina almost 2 years ago - 1 comment
Labels: bug

#36 - python >= 3.8

Pull Request - State: closed - Opened by Robaina almost 2 years ago
Labels: enhancement

#35 - Add codecov to github action

Issue - State: closed - Opened by Robaina almost 2 years ago - 1 comment
Labels: enhancement

#33 - Create a devcontainer for codespaces?

Issue - State: closed - Opened by Robaina almost 2 years ago - 2 comments
Labels: enhancement

#32 - Python version lower than 3.10?

Issue - State: closed - Opened by Robaina almost 2 years ago
Labels: enhancement

#31 - Prepare GitHub Action for CI

Issue - State: closed - Opened by Robaina almost 2 years ago - 1 comment
Labels: enhancement

#30 - 28-change-docstring-format-to-google-format

Pull Request - State: closed - Opened by Robaina almost 2 years ago - 1 comment

#29 - Deal with genome ID when building peptide database from genbank files

Issue - State: closed - Opened by Robaina almost 2 years ago - 1 comment
Labels: enhancement

#28 - Change docstring format to Google format

Issue - State: closed - Opened by Robaina almost 2 years ago
Labels: documentation, enhancement

#27 - Double check peptide labels in database

Issue - State: closed - Opened by Robaina almost 2 years ago
Labels: enhancement

#26 - Add code snippets from examples in README.md

Issue - State: closed - Opened by Robaina almost 2 years ago
Labels: documentation

#25 - Check docstrings

Issue - State: closed - Opened by Robaina almost 2 years ago - 1 comment
Labels: documentation

#24 - Making Pynteny pip-installable

Issue - State: closed - Opened by Robaina almost 2 years ago - 1 comment
Labels: enhancement, refactor

#23 - Create online documentation

Issue - State: closed - Opened by Robaina almost 2 years ago - 1 comment
Labels: enhancement

#22 - Restructure Project

Issue - State: closed - Opened by Robaina almost 2 years ago
Labels: refactor

#21 - Pynteny search results table: sorting when "--unordered"

Issue - State: closed - Opened by Robaina about 2 years ago - 3 comments

#20 - Incomplete documentation for --unordered

Issue - State: closed - Opened by Robaina about 2 years ago - 1 comment

#19 - Add search optional parameter to reuse hmmer search result tables

Pull Request - State: closed - Opened by Robaina about 2 years ago - 1 comment

#18 - Add search optional parameter to reuse hmmer search result tables

Issue - State: closed - Opened by Robaina about 2 years ago
Labels: enhancement

#17 - File manager not showing up correctly in Firefox

Issue - State: closed - Opened by Robaina about 2 years ago - 1 comment
Labels: bug

#16 - Enable unordered HMM search (synteny vs collinearity)

Pull Request - State: closed - Opened by Robaina about 2 years ago

#14 - Include prodigal translation in Database object

Issue - State: closed - Opened by Robaina over 2 years ago - 1 comment
Labels: refactor

#13 - Remove missing (from PGAP directory) entries from PGAP meta data upon donwload

Issue - State: closed - Opened by Robaina over 2 years ago - 1 comment
Labels: bug

#12 - Save log to text file

Issue - State: closed - Opened by Robaina over 2 years ago - 1 comment
Labels: enhancement

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

Issue - State: closed - Opened by Robaina over 2 years ago - 1 comment
Labels: enhancement

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

Issue - State: closed - Opened by Robaina over 2 years ago - 1 comment
Labels: bug

#7 - Add meta info to hits when provided

Issue - State: closed - Opened by Robaina over 2 years ago - 2 comments
Labels: enhancement

#6 - Allow initializing preprocess with multiple GenBank/FASTA files

Issue - State: closed - Opened by Robaina over 2 years ago - 1 comment
Labels: enhancement

#5 - Use python logger instead of print statements

Issue - State: closed - Opened by Robaina over 2 years ago - 1 comment
Labels: enhancement

#4 - Final output hmm name tags may be misleading when employing alternative hmm names for same target

Issue - State: closed - Opened by Robaina over 2 years ago - 1 comment
Labels: bug, invalid

#3 - Provide meaningful use case

Issue - State: closed - Opened by Robaina over 2 years ago - 1 comment
Labels: enhancement

#2 - Dev

Pull Request - State: closed - Opened by Robaina over 2 years ago

#1 - Dev

Pull Request - State: closed - Opened by Robaina over 2 years ago

GitHub / Robaina/Pynteny issues and pull requests