PoonLab Poplars issues - Githubissues

PoonLab / Poplars

Open-source implementations of popular tools from Los Alamos National Laboratory HIV Database

GNU Affero General Public License v3.0

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hypermut: improve output format

#40 ArtPoon opened 3 years ago
0
potential fix for #38

#39 ArtPoon closed 3 years ago
1
sequence_locator: does not accept mixtures

#38 ArtPoon opened 3 years ago
0
sequence_locator: internal use case

#37 ArtPoon opened 3 years ago
0
sequence_locator: missing data file

#36 ArtPoon opened 3 years ago
1
sequence_locator: alignment error and additional outputs

#35 ArtPoon opened 3 years ago
2
sequence_locator.py: Allow more easily parsable output

#34 kwade4 closed 4 years ago
0
sequence_locator.py: Handle multiple input sequences

#33 kwade4 closed 4 years ago
0
Sequence locator: super() error

#32 ArtPoon closed 4 years ago
1
sequence_locator.py: Improve command line interface

#31 kwade4 closed 4 years ago
0
riplike: TypeError

#30 ArtPoon opened 5 years ago
0
hypermut.py: Make console output easier to parse

#29 kwade4 closed 5 years ago
1
hypermut: no indication of reference sequence

#28 ArtPoon closed 5 years ago
1
sequence_locator: cmd line interface unclear

#27 ArtPoon closed 5 years ago
1
hypermut: Check for aligned sequences

#26 kwade4 closed 5 years ago
0
riplike: Handle ambiguous nucleotides

#25 kwade4 opened 5 years ago
0
common.py: fails second test case

#24 kwade4 closed 5 years ago
0
sequence_locator: Each region object should store local and global coordinates

#23 kwade4 closed 5 years ago
1
Look into converting sequences into bit strings

#22 ArtPoon opened 5 years ago
5
Drop scipy as dependency and implement Fisher's exact test

#21 ArtPoon closed 5 years ago
2
sequence_locator: "retrieve" gives incorrect regions and region coordinates

#20 kwade4 opened 5 years ago
1
riplike: user-defined background alignment

#19 kwade4 closed 5 years ago
0
sequence_locator.py: Update local alignment algorithm

#18 kwade4 closed 5 years ago
4
riplike should produce nucleotide-level calls

#17 ArtPoon closed 5 years ago
2
sequence_locator: unusual outputs

#16 ArtPoon closed 5 years ago
0
sequence_locator: rejects query sequence containing gaps

#15 ArtPoon closed 5 years ago
0
sequence_locator: goofy help text

#14 ArtPoon closed 5 years ago
0
riplike: conduct tests

#13 ArtPoon opened 5 years ago
2
riplike: script is too slow compared to LANL tool

#12 ArtPoon opened 5 years ago
5
Remove Biopython dependency in hypermut.py

#11 kwade4 closed 5 years ago
0
Remove hard-coded absolute path from unittest

#10 ArtPoon closed 5 years ago
0
Create a list of accession numbers for reference genomes and test data

#9 kwade4 closed 5 years ago
1
Implement SequenceLocator script

#8 ArtPoon closed 3 years ago
1
Merge dev into master

#7 kwade4 closed 5 years ago
0
sequence_locator: Fix reference and tempfile path names

#6 kwade4 closed 5 years ago
1
make /bin directory for open-source binary dependencies

#5 ArtPoon closed 5 years ago
12
Python implementation of poisson-fitter v2

#4 kwade4 closed 5 years ago
3
hypermut: modify output to pass p-values to poisson-fitter

#3 kwade4 closed 5 years ago
0
riplike: remove MAFFT as dependency?

#2 ArtPoon closed 5 years ago
1
riplike: make consistent ref coordinates across outputs

#1 ArtPoon opened 5 years ago
0