Ecosyste.ms: Issues

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

GitHub / wilkelab/Opfi issues and pull requests

#213 - adding transposon gene location in operon_analyzer

Issue - State: open - Opened by Jigyasa3 over 1 year ago - 2 comments

#212 - Release 0.1.2

Pull Request - State: closed - Opened by alexismhill3 over 3 years ago

#211 - Add JOSS editor revisions to Opfi paper

Pull Request - State: closed - Opened by alexismhill3 over 3 years ago

#210 - Add reference for Bioconda

Pull Request - State: closed - Opened by alexismhill3 over 3 years ago

#209 - Paper review

Pull Request - State: closed - Opened by alexismhill3 over 3 years ago

#208 - Remove modified PILER-CR source code

Pull Request - State: closed - Opened by alexismhill3 over 3 years ago

#207 - Make Opfi available on Bioconda

Pull Request - State: closed - Opened by alexismhill3 over 3 years ago

#206 - Import style

Issue - State: open - Opened by afrubin over 3 years ago

#205 - "Operons"

Issue - State: open - Opened by afrubin over 3 years ago

#204 - Flatten `tutorials/` into a single-level directory

Pull Request - State: closed - Opened by alexismhill3 over 3 years ago - 1 comment

#203 - Tutorial example 1 crashes

Issue - State: closed - Opened by Thomieh73 over 3 years ago

#202 - Installation using a conda environment

Issue - State: closed - Opened by Thomieh73 over 3 years ago

#201 - Documentation for optional dependencies

Issue - State: closed - Opened by afrubin over 3 years ago - 1 comment

#200 - Installation in docs vs. README

Issue - State: closed - Opened by afrubin over 3 years ago

#199 - Platform requirements

Issue - State: closed - Opened by afrubin over 3 years ago

#198 - PILER-CR requirement

Issue - State: closed - Opened by afrubin over 3 years ago

#197 - Release 0.1.0

Pull Request - State: closed - Opened by alexismhill3 over 3 years ago

#196 - fix inaccurate description of pytest usage

Pull Request - State: closed - Opened by alexismhill3 over 3 years ago

#195 - Paper

Pull Request - State: closed - Opened by alexismhill3 over 3 years ago

#194 - Paper

Pull Request - State: closed - Opened by alexismhill3 over 3 years ago

#193 - Opfi documentation site

Pull Request - State: closed - Opened by alexismhill3 over 3 years ago

#192 - Bump pyyaml from 5.3.1 to 5.4

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago
Labels: dependencies

#191 - Contributing guide

Pull Request - State: closed - Opened by alexismhill3 over 3 years ago

#190 - Clean up project root directory and add a tutorial for Opfi

Pull Request - State: closed - Opened by alexismhill3 over 3 years ago

#189 - update third operon_analyzer example

Pull Request - State: closed - Opened by jimrybarski over 3 years ago

#187 - Allow more information about genes to be displayed in gene diagrams

Pull Request - State: closed - Opened by jimrybarski over 3 years ago

#186 - Update readme

Pull Request - State: closed - Opened by alexismhill3 over 3 years ago

#185 - Gene finder cleanup

Pull Request - State: closed - Opened by alexismhill3 over 3 years ago

#184 - Refactor plotting function

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

#183 - Add spacer position, don't allow spacers to target themselves

Pull Request - State: closed - Opened by jimrybarski about 4 years ago

#182 - Deduplicate supersets

Pull Request - State: closed - Opened by jimrybarski about 4 years ago

#181 - Prevent temp file from being created in source directory

Issue - State: closed - Opened by jimrybarski about 4 years ago - 1 comment

#180 - Add maximum size rule

Pull Request - State: closed - Opened by jimrybarski about 4 years ago

#179 - Use correct substitution matrix

Pull Request - State: closed - Opened by jimrybarski about 4 years ago

#178 - Document which array targets a CRISPR target

Issue - State: closed - Opened by jimrybarski about 4 years ago

#177 - Fix newline error in as_str

Pull Request - State: closed - Opened by jimrybarski about 4 years ago

#176 - Fix invalid import

Pull Request - State: closed - Opened by jimrybarski about 4 years ago

#175 - Nicer summary API

Pull Request - State: closed - Opened by jimrybarski over 4 years ago

#174 - Remove the newline after serializing an operon

Pull Request - State: closed - Opened by jimrybarski over 4 years ago

#173 - Fix sts

Pull Request - State: closed - Opened by jimrybarski over 4 years ago

#172 - Allow ignoring of features to persist when serialized

Issue - State: closed - Opened by jimrybarski over 4 years ago - 1 comment
Labels: enhancement

#171 - Repeat finder

Pull Request - State: closed - Opened by jimrybarski over 4 years ago

#170 - Allow user to set path to BLAST

Pull Request - State: closed - Opened by jimrybarski over 4 years ago

#169 - Don't give a direction to CRISPR arrays

Pull Request - State: closed - Opened by jimrybarski over 4 years ago

#168 - Add rule to apply minimum length to genes.

Pull Request - State: closed - Opened by jimrybarski over 4 years ago

#167 - Fix feature length

Pull Request - State: closed - Opened by jimrybarski over 4 years ago

#166 - Serialize operons

Pull Request - State: closed - Opened by jimrybarski over 4 years ago

#165 - Consistent indices

Pull Request - State: closed - Opened by jimrybarski over 4 years ago

#164 - Self targeting spacer search

Pull Request - State: closed - Opened by jimrybarski over 4 years ago - 2 comments

#163 - Deduplication of operons

Pull Request - State: closed - Opened by jimrybarski over 4 years ago

#162 - Temporarily disable property-based tests

Pull Request - State: closed - Opened by jimrybarski over 4 years ago

#161 - Remove redundant operons by seq

Pull Request - State: closed - Opened by jimrybarski over 4 years ago

#160 - Fix blastn strand

Pull Request - State: closed - Opened by jimrybarski over 4 years ago
Labels: bug

#159 - Provide access to an operon's nucleotide sequence

Pull Request - State: closed - Opened by jimrybarski over 4 years ago

#158 - Add nucleotide BLAST step

Pull Request - State: closed - Opened by jimrybarski over 4 years ago

#157 - Fix blast type bug

Pull Request - State: closed - Opened by jimrybarski over 4 years ago

#156 - truncate cluster names for really long operons

Pull Request - State: closed - Opened by alexismhill3 over 4 years ago - 2 comments

#155 - Allow diagram line wrapping

Pull Request - State: closed - Opened by alexismhill3 over 4 years ago

#154 - Make contains_group() case-insensitive

Pull Request - State: closed - Opened by jimrybarski over 4 years ago

#153 - Fix bug that may cause _contains_group to return False prematurely

Pull Request - State: closed - Opened by alexismhill3 over 4 years ago

#152 - Prevent redundant operons from being loaded

Pull Request - State: closed - Opened by jimrybarski over 4 years ago - 2 comments

#151 - Eliminate redundant operons

Issue - State: closed - Opened by jimrybarski over 4 years ago

#149 - `contains_group` should not be case sensitive

Issue - State: closed - Opened by jimrybarski over 4 years ago
Labels: bug

#148 - Add a missing interface to the contains_group rule

Pull Request - State: closed - Opened by jimrybarski over 4 years ago

#147 - Add a rule to find contiguous groups of features.

Pull Request - State: closed - Opened by jimrybarski over 4 years ago

#146 - Rule for groups of features

Issue - State: closed - Opened by jimrybarski over 4 years ago

#145 - Let user define buffer around features when plotting operons

Issue - State: closed - Opened by jimrybarski over 4 years ago - 1 comment
Labels: enhancement

#144 - Use sys.float_info.min instead of epsilon

Pull Request - State: closed - Opened by jimrybarski over 4 years ago - 1 comment

#143 - crash when making BLAST-statistic colormap plots

Issue - State: closed - Opened by jimrybarski over 4 years ago
Labels: bug

#142 - Better color bounds definition

Pull Request - State: closed - Opened by jimrybarski over 4 years ago

#141 - Color stacked plots by BLAST statistic.

Pull Request - State: closed - Opened by jimrybarski over 4 years ago

#140 - Creates the correct directory.

Pull Request - State: closed - Opened by jimrybarski over 4 years ago

#138 - Incorrect subdirectory creation

Issue - State: closed - Opened by jimrybarski over 4 years ago
Labels: bug

#137 - color by BLAST statistic in clustered stacked plots

Issue - State: closed - Opened by jimrybarski over 4 years ago

#136 - Provide an option to incrementally write Gene Finder output to disk

Pull Request - State: closed - Opened by alexismhill3 over 4 years ago - 1 comment

#124 - operon analyzer cleanup

Issue - State: closed - Opened by jimrybarski over 4 years ago - 2 comments

#121 - Allow Gene Finder to accept arbitrary blast command flags

Pull Request - State: closed - Opened by alexismhill3 over 4 years ago

#114 - allow the user to optionally specify a path to the search utility

Issue - State: closed - Opened by alexismhill3 over 4 years ago - 2 comments

#112 - Add an option to use the whole reference protein description as the gene label

Pull Request - State: closed - Opened by alexismhill3 over 4 years ago - 2 comments

#104 - Update gene finder portion of the README

Issue - State: closed - Opened by alexismhill3 over 4 years ago

#103 - Opfi should be briefly described in the README

Issue - State: closed - Opened by alexismhill3 over 4 years ago

#102 - Rename crisposon to Opfi

Pull Request - State: closed - Opened by alexismhill3 over 4 years ago

#94 - Merge code freeze into master

Pull Request - State: closed - Opened by jimrybarski over 4 years ago - 2 comments

#69 - update installer

Pull Request - State: closed - Opened by jimrybarski over 4 years ago

#63 - Only modify CRISPR array names for visualization

Pull Request - State: closed - Opened by jimrybarski over 4 years ago - 1 comment

#58 - Fully test and document optional pipeline setup arguments

Issue - State: closed - Opened by alexismhill3 over 4 years ago
Labels: documentation, tests

#45 - Mark location of unannotated ORFs in the operon

Issue - State: closed - Opened by jimrybarski over 4 years ago - 1 comment
Labels: enhancement

#36 - Allow user to choose to display ignored features

Pull Request - State: closed - Opened by jimrybarski over 4 years ago

#33 - Automatically install wheel if it's not present already during setup

Pull Request - State: closed - Opened by jimrybarski almost 5 years ago

#30 - Document sequence identifier requirements

Issue - State: closed - Opened by jimrybarski almost 5 years ago - 2 comments
Labels: documentation

#29 - Add pytest as a dependency

Pull Request - State: closed - Opened by jimrybarski almost 5 years ago

#23 - Better annotation of fused genes

Issue - State: closed - Opened by alexismhill3 almost 5 years ago
Labels: enhancement, wontfix

#21 - More informative and cleaner logging

Issue - State: closed - Opened by alexismhill3 almost 5 years ago
Labels: wontfix, maintenance

#14 - Integration tests

Issue - State: closed - Opened by alexismhill3 almost 5 years ago
Labels: tests

#12 - Unit tests for orffinder module

Issue - State: closed - Opened by alexismhill3 almost 5 years ago
Labels: tests

#11 - unit tests for blast output parsing

Issue - State: closed - Opened by alexismhill3 almost 5 years ago
Labels: tests