Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / PoonLab/sierra-local issues and pull requests

#103 - New release

Issue - State: closed - Opened by raquelriyuzo 7 months ago - 2 comments

#102 - fixed import error from removing subtyper script

Pull Request - State: closed - Opened by WilliamZekaiWang 10 months ago

#101 - Subtyper module

Issue - State: closed - Opened by Kanyerezi30 10 months ago - 2 comments

#100 - fixes to #99 and deprecating subtyping

Pull Request - State: closed - Opened by WilliamZekaiWang 10 months ago

#99 - NRTI resistance profile

Issue - State: closed - Opened by Kanyerezi30 10 months ago - 3 comments

#98 - Issue 72 fix for NNN nucleotides

Pull Request - State: closed - Opened by WilliamZekaiWang 12 months ago

#97 - Iss72

Pull Request - State: closed - Opened by WilliamZekaiWang 12 months ago

#96 - Unkown subtype

Issue - State: closed - Opened by erick-dorlass about 1 year ago - 6 comments

#95 - fixes to isInsertion (issue #91)

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

#94 - JSON to CSV conversion Error: json2csv.py

Issue - State: closed - Opened by gpcr about 1 year ago - 5 comments

#93 - fixes to #92

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

#92 - TypeError: unsupported operand type(s) for -: 'int' and 'NoneType'

Issue - State: closed - Opened by aguang about 1 year ago - 2 comments

#91 - Missing T69S_SS (T69ins) mutation

Issue - State: closed - Opened by Kanyerezi30 about 1 year ago - 10 comments

#90 - DOR resistance level

Issue - State: closed - Opened by Kanyerezi30 about 1 year ago - 3 comments

#89 - setup.py and postalign

Issue - State: closed - Opened by aguang about 1 year ago - 2 comments

#88 - Updating Post-align Dependencies

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

#87 - postalign vs nucamino

Issue - State: closed - Opened by Kanyerezi30 over 1 year ago - 11 comments

#86 - Adding subtyping option and fixes to -json

Pull Request - State: closed - Opened by WilliamZekaiWang over 1 year ago - 4 comments

#85 - Subtyping

Issue - State: closed - Opened by Kanyerezi30 over 1 year ago - 2 comments

#83 - Adding Postalign as Alignment Program

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

#82 - Switch to postalign and updating unit tests, resources

Pull Request - State: closed - Opened by ArtPoon over 1 year ago - 2 comments

#81 - Add postalign as a submodule

Issue - State: closed - Opened by ArtPoon over 1 year ago

#78 - Update dev branch with recent changes

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

#77 - Issue when testing `align_file` method of `NucAminoAligner`

Issue - State: closed - Opened by SandeepThokala over 1 year ago - 1 comment

#76 - Issue with `scorerange` parameter of `parse_globalrange` method

Issue - State: closed - Opened by SandeepThokala over 1 year ago - 3 comments

#72 - Fail to run with iupac codes

Issue - State: closed - Opened by erick-dorlass almost 2 years ago - 19 comments

#71 - Alignment Program

Issue - State: closed - Opened by Kanyerezi30 almost 2 years ago - 22 comments

#70 - list index out of range for hivdb versions 9.3 and 9.4

Issue - State: closed - Opened by Kanyerezi30 almost 2 years ago - 4 comments

#69 - Incorrect NA sequence from nucamino

Issue - State: closed - Opened by WilliamZekaiWang almost 2 years ago - 4 comments

#68 - Use submodule to retrieve data files

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

#67 - AttributeError: 'xml.etree.ElementTree.Element' object has no attribute 'getchildren'

Issue - State: closed - Opened by ArtPoon almost 2 years ago - 8 comments

#66 - Failure to update HIVDB and APOBEC DRMS

Issue - State: closed - Opened by Kanyerezi30 almost 2 years ago - 5 comments

#65 - Sierra-local output file does not match with Sierrapy

Issue - State: closed - Opened by GopiGugan about 2 years ago - 18 comments

#64 - Problem running updater script

Issue - State: closed - Opened by ArtPoon over 2 years ago - 6 comments

#63 - User request: support AAVF or CodFreq input file formats

Issue - State: open - Opened by ArtPoon over 3 years ago - 1 comment
Labels: enhancement

#62 - Write unit test suite

Issue - State: closed - Opened by ArtPoon about 5 years ago - 6 comments

#61 - HIVdb algorithm initialization code is in JSONWriter

Issue - State: open - Opened by ArtPoon about 5 years ago
Labels: help wanted

#60 - Distribute ASI2 XML to improve user experience

Issue - State: closed - Opened by ArtPoon about 5 years ago

#59 - HIVdb swiched from static to dynamic HTML for DRM ASI2 files

Issue - State: closed - Opened by ArtPoon about 5 years ago - 1 comment

#58 - HIVdb assets blocked with 403

Issue - State: closed - Opened by ArtPoon about 5 years ago

#57 - sierralocal fails on macOS High Sierra with Python 3.7.4

Issue - State: closed - Opened by ArtPoon about 5 years ago - 1 comment

#56 - Stanford HIVdb moved data sets

Issue - State: closed - Opened by ArtPoon about 5 years ago

#55 - installation tests

Issue - State: closed - Opened by ghost over 5 years ago - 4 comments

#54 - PEP8 compliance

Issue - State: closed - Opened by ArtPoon almost 6 years ago - 2 comments

#53 - [JOSS review] sierrapy reference

Issue - State: closed - Opened by azneto almost 6 years ago

#52 - [JOSS review] community guidelines

Issue - State: closed - Opened by azneto almost 6 years ago - 1 comment

#51 - Installation from PyPI (pip) failed on fresh Ubuntu workstation

Issue - State: closed - Opened by ArtPoon about 6 years ago - 1 comment

#50 - sequences with long upstream sequence including deletions are incorrectly subtyped

Issue - State: closed - Opened by ArtPoon about 6 years ago - 2 comments
Labels: bug, help wanted

#49 - script does not run new XML following forceupdate

Issue - State: closed - Opened by ArtPoon about 6 years ago - 1 comment

#48 - Need to adjust coordinates for sequences spanning multiple regions

Issue - State: closed - Opened by ArtPoon about 6 years ago - 1 comment

#47 - Not scoring deletions correctly

Issue - State: closed - Opened by ArtPoon about 6 years ago

#46 - Hard-to-reach binary for macOS installation from source via MacPorts

Issue - State: closed - Opened by ArtPoon about 6 years ago - 1 comment

#45 - sierralocal fails on full-length pol sequence

Issue - State: closed - Opened by ArtPoon about 6 years ago - 6 comments

#44 - Subtyping slows down pipeline substantially

Issue - State: closed - Opened by ArtPoon about 6 years ago - 8 comments

#43 - Allow user to specify local NucAmino binary and XML, data files

Issue - State: closed - Opened by ArtPoon about 6 years ago - 1 comment
Labels: enhancement

#42 - XML woes

Issue - State: closed - Opened by sdwfrost about 6 years ago - 13 comments

#41 - Refactoring broke genotyping of INT sequences

Issue - State: closed - Opened by ArtPoon about 6 years ago - 1 comment

#40 - subtyper doesn't work, requires aligned sequences

Issue - State: closed - Opened by ArtPoon about 6 years ago

#39 - Sequence mapped to RNAse

Issue - State: closed - Opened by ArtPoon about 6 years ago - 6 comments

#38 - Subtyping script fails on one item

Issue - State: closed - Opened by ArtPoon about 6 years ago - 1 comment

#37 - Re-run validation experiments with refactored package

Issue - State: closed - Opened by ArtPoon about 6 years ago

#36 - Loss of speed in latest commit

Issue - State: closed - Opened by ArtPoon about 6 years ago - 4 comments

#35 - testing pip3 install on fresh Ubuntu installation

Issue - State: closed - Opened by ArtPoon about 6 years ago - 4 comments
Labels: bug

#34 - GUI script broken

Issue - State: closed - Opened by ArtPoon about 6 years ago - 2 comments

#33 - Installation on macOS

Issue - State: closed - Opened by ArtPoon about 6 years ago - 4 comments

#32 - Script should automatically run update

Issue - State: closed - Opened by ArtPoon over 6 years ago

#31 - Provide JSON viewer (HTML)

Issue - State: open - Opened by ArtPoon over 6 years ago - 1 comment
Labels: enhancement

#30 - Convert to Python module

Issue - State: closed - Opened by ArtPoon over 6 years ago

#29 - Move subtyper.py to another branch

Issue - State: closed - Opened by ArtPoon over 6 years ago - 2 comments

#28 - Create LICENSE

Pull Request - State: closed - Opened by ArtPoon over 6 years ago

#27 - Update installation instructions

Issue - State: closed - Opened by ArtPoon over 6 years ago - 3 comments

#26 - Sequence Subtyping

Issue - State: closed - Opened by jzpero over 6 years ago - 2 comments
Labels: low priority

#25 - Trim low quality nucleotides in the start and end of each sequence

Issue - State: closed - Opened by jzpero over 6 years ago - 5 comments
Labels: enhancement

#24 - OOP design

Issue - State: closed - Opened by jzpero over 6 years ago - 3 comments

#23 - Make GUI with Tkinter?

Issue - State: closed - Opened by ArtPoon over 6 years ago - 3 comments
Labels: enhancement

#22 - Switch to platform-independent paths

Issue - State: closed - Opened by jzpero over 6 years ago - 4 comments

#21 - Query frameshift gap (~) issues

Issue - State: closed - Opened by jzpero over 6 years ago - 6 comments

#20 - Score maximization bug

Issue - State: closed - Opened by jzpero over 6 years ago
Labels: bug

#19 - Mutation mixtures being scored more than once

Issue - State: closed - Opened by jzpero over 6 years ago
Labels: bug

#18 - User issues

Issue - State: closed - Opened by ArtPoon over 6 years ago

#17 - Pull comments files dynamically

Issue - State: open - Opened by ArtPoon almost 7 years ago - 3 comments
Labels: enhancement, low priority

#16 - Clean up repo

Issue - State: closed - Opened by ArtPoon almost 7 years ago

#15 - Validation status

Issue - State: closed - Opened by jzpero almost 7 years ago - 3 comments

#14 - Polymorphism interpretation

Issue - State: closed - Opened by jzpero almost 7 years ago - 2 comments

#13 - Sequence offset contributing to errors in mutation scoring

Issue - State: closed - Opened by jzpero almost 7 years ago - 1 comment

#12 - Classification of mutations (to-do)

Issue - State: closed - Opened by jzpero almost 7 years ago - 3 comments

#11 - Validation against sierra-client

Issue - State: closed - Opened by ArtPoon almost 7 years ago - 6 comments

#10 - Regex matching negative scores

Issue - State: closed - Opened by jzpero about 7 years ago - 2 comments
Labels: help wanted

#9 - Incorporate Stanford HIVDB's NucAmino aligner?

Issue - State: closed - Opened by ArtPoon about 7 years ago - 4 comments
Labels: question

#8 - Scoring algorithm results not matching with HIVdb output

Issue - State: closed - Opened by jzpero about 7 years ago - 4 comments

#7 - Insertions relative to reference need to be recorded for scoring

Issue - State: closed - Opened by ArtPoon about 7 years ago - 2 comments

#6 - Plan return object (data structure) from scoring script

Issue - State: closed - Opened by ArtPoon about 7 years ago - 4 comments

#5 - parse_definitions may not be robust

Issue - State: closed - Opened by MathiasRenaud over 7 years ago - 1 comment