widdowquinn ncfp issues

widdowquinn / ncfp

Program and package that retrieves nucleotide coding sequences from NCBI that correspond to a set of input protein sequences.

https://widdowquinn.github.io/ncfp/

MIT License

3 stars 2 forks source link

issues

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Issue 50

#51 widdowquinn closed 4 months ago
0
Move CI to GitHub Actions

#50 widdowquinn closed 4 months ago
0
Not identifying CDS and removed or suppressed by NCBI

#49 tharis opened 5 months ago
0
Issue 46

#48 widdowquinn closed 5 months ago
0
Make `ncfp.py` less complex

#47 widdowquinn opened 5 months ago
0
Not identifying CDS feature despite feature existing

#46 tharis closed 5 months ago
3
Biopython DeprecationWarning for ungap() Method

#45 monserrj closed 4 months ago
1
List index out of range when processing sequences

#44 widdowquinn closed 1 year ago
1
UniProt protein ID is available but not used for resolution of ambiguous gene names

#43 widdowquinn opened 2 years ago
0
Partial fix for #41

#42 widdowquinn closed 1 year ago
1
When multiple possible CDS matches are found, sometimes the 'wrong one' is processed.

#41 widdowquinn opened 2 years ago
0
update CHANGES.md

#40 widdowquinn closed 2 years ago
0
allow recovery of input sequences requiring GeneID

#39 widdowquinn closed 2 years ago
0
fix issue with UniProt API query

#38 widdowquinn closed 2 years ago
0
Issue 34: add option to allow alternative start sites

#37 widdowquinn closed 2 years ago
2
log warning, but don't raise error, when record is missing/suppressed

#36 widdowquinn closed 2 years ago
1
UniProt warning

#35 widdowquinn closed 2 years ago
2
Error occuring when ncfp encounters sequences which have been removed from NCBI database

#34 ArtingBioinfo opened 2 years ago
6
Documentation no longer reflects CLI for `-u` option

#33 widdowquinn opened 2 years ago
0
fix issue #31

#32 widdowquinn closed 2 years ago
1
Incorrect protein sequences being retrieved for some accessions

#31 widdowquinn closed 2 years ago
2
Issue 24

#30 widdowquinn closed 2 years ago
1
Issue 25

#29 widdowquinn closed 2 years ago
1
fixes issue #27

#28 widdowquinn closed 2 years ago
1
Stockholm domain format doesn't work with non-UniProt FASTA sequences

#27 widdowquinn closed 2 years ago
0
Tests indicate a deprecated method

#26 widdowquinn closed 2 years ago
2
Writing log file fails if only filename given

#25 widdowquinn closed 2 years ago
1
Add an indicator of total steps to progress bars

#24 widdowquinn closed 2 years ago
0
Drop terminal stop codons

#23 HobnobMancer opened 2 years ago
3
Issue 21 protein ids

#22 HobnobMancer closed 2 years ago
5
Use protein IDs in output

#21 HobnobMancer closed 2 years ago
0
`ncfp` not recovering all coding sequences from NCBI

#20 widdowquinn closed 2 years ago
2
Fixes Issue #18

#19 widdowquinn closed 3 years ago
1
CircleCI test error: Entrez calls failing

#18 widdowquinn closed 3 years ago
0
Mock remote service calls in tests

#17 widdowquinn opened 4 years ago
2
Resolve #13

#16 widdowquinn closed 4 years ago
1
Upgrade schema/interface for cache

#15 widdowquinn opened 4 years ago
1
Implement batching/retries for downloads as decorators

#14 widdowquinn opened 4 years ago
0
Revise tests to use `pytest` features

#13 widdowquinn closed 4 years ago
0
Update ncfp for the move to Strathclyde

#12 widdowquinn closed 4 years ago
1
Add ability to pull down upstream sequences

#11 widdowquinn opened 4 years ago
0
Add a Codacy badge to README.md

#10 codacy-badger closed 6 years ago
1
Docs

#9 widdowquinn closed 6 years ago
0
Sphinxdocs

#8 widdowquinn closed 6 years ago
1
Sphinxdocs

#7 widdowquinn closed 6 years ago
0
Sphinxdocs

#6 widdowquinn closed 6 years ago
0
Sphinxdocs

#5 widdowquinn closed 6 years ago
0
Sphinxdocs

#4 widdowquinn closed 6 years ago
0
Sphinxdocs

#3 widdowquinn closed 6 years ago
0
Sphinxdocs

#2 widdowquinn closed 6 years ago
0