widdowquinn/ncfp issues and pull requests

#51 - Issue 50

Pull Request - State: closed - Opened by widdowquinn 3 months ago

#50 - Move CI to GitHub Actions

Issue - State: closed - Opened by widdowquinn 3 months ago
Labels: enhancement, testing

#49 - Not identifying CDS and removed or suppressed by NCBI

Issue - State: open - Opened by tharis 4 months ago

#48 - Issue 46

Pull Request - State: closed - Opened by widdowquinn 4 months ago

#47 - Make `ncfp.py` less complex

Issue - State: open - Opened by widdowquinn 4 months ago
Labels: enhancement

#46 - Not identifying CDS feature despite feature existing

Issue - State: closed - Opened by tharis 5 months ago - 3 comments
Labels: bug

#45 - Biopython DeprecationWarning for ungap() Method

Issue - State: closed - Opened by monserrj 10 months ago - 1 comment
Labels: bug

#44 - List index out of range when processing sequences

Issue - State: closed - Opened by widdowquinn 12 months ago - 1 comment
Labels: bug

#43 - UniProt protein ID is available but not used for resolution of ambiguous gene names

Issue - State: open - Opened by widdowquinn about 2 years ago
Labels: bug

#42 - Partial fix for #41

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

#41 - When multiple possible CDS matches are found, sometimes the 'wrong one' is processed.

Issue - State: open - Opened by widdowquinn about 2 years ago
Labels: bug

#40 - update CHANGES.md

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

#39 - allow recovery of input sequences requiring GeneID

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

#38 - fix issue with UniProt API query

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

#37 - Issue 34: add option to allow alternative start sites

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

#36 - log warning, but don't raise error, when record is missing/suppressed

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

#35 - UniProt warning

Issue - State: closed - Opened by widdowquinn about 2 years ago - 2 comments
Labels: bug

#34 - Error occuring when ncfp encounters sequences which have been removed from NCBI database

Issue - State: open - Opened by ArtingBioinfo about 2 years ago - 6 comments
Labels: bug

#33 - Documentation no longer reflects CLI for `-u` option

Issue - State: open - Opened by widdowquinn over 2 years ago
Labels: documentation

#32 - fix issue #31

Pull Request - State: closed - Opened by widdowquinn over 2 years ago - 1 comment

#31 - Incorrect protein sequences being retrieved for some accessions

Issue - State: closed - Opened by widdowquinn over 2 years ago - 2 comments
Labels: bug

#30 - Issue 24

Pull Request - State: closed - Opened by widdowquinn over 2 years ago - 1 comment

#29 - Issue 25

Pull Request - State: closed - Opened by widdowquinn over 2 years ago - 1 comment

#28 - fixes issue #27

Pull Request - State: closed - Opened by widdowquinn over 2 years ago - 1 comment

#27 - Stockholm domain format doesn't work with non-UniProt FASTA sequences

Issue - State: closed - Opened by widdowquinn over 2 years ago
Labels: bug, enhancement

#26 - Tests indicate a deprecated method

Issue - State: closed - Opened by widdowquinn over 2 years ago - 2 comments
Labels: bug, enhancement

#25 - Writing log file fails if only filename given

Issue - State: closed - Opened by widdowquinn over 2 years ago - 1 comment
Labels: bug, cannot reproduce

#24 - Add an indicator of total steps to progress bars

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

#23 - Drop terminal stop codons

Issue - State: open - Opened by HobnobMancer over 2 years ago - 3 comments
Labels: enhancement

#22 - Issue 21 protein ids

Pull Request - State: closed - Opened by HobnobMancer over 2 years ago - 5 comments
Labels: enhancement

#21 - Use protein IDs in output

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

#20 - `ncfp` not recovering all coding sequences from NCBI

Issue - State: closed - Opened by widdowquinn almost 3 years ago - 2 comments
Labels: bug

#19 - Fixes Issue #18

Pull Request - State: closed - Opened by widdowquinn over 3 years ago - 1 comment
Labels: testing

#18 - CircleCI test error: Entrez calls failing

Issue - State: closed - Opened by widdowquinn over 3 years ago
Labels: testing

#17 - Mock remote service calls in tests

Issue - State: open - Opened by widdowquinn about 4 years ago - 2 comments
Labels: testing

#16 - Resolve #13

Pull Request - State: closed - Opened by widdowquinn about 4 years ago - 1 comment
Labels: enhancement, testing

#15 - Upgrade schema/interface for cache

Issue - State: open - Opened by widdowquinn about 4 years ago - 1 comment
Labels: enhancement

#14 - Implement batching/retries for downloads as decorators

Issue - State: open - Opened by widdowquinn about 4 years ago
Labels: enhancement

#13 - Revise tests to use `pytest` features

Issue - State: closed - Opened by widdowquinn about 4 years ago
Labels: enhancement, testing

#12 - Update ncfp for the move to Strathclyde

Pull Request - State: closed - Opened by widdowquinn about 4 years ago - 1 comment

#11 - Add ability to pull down upstream sequences

Issue - State: open - Opened by widdowquinn over 4 years ago
Labels: enhancement