phageParser/phageParser issues and pull requests

#289 - Change instructions for installing xerces-c

Issue - State: open - Opened by bganglia almost 5 years ago - 1 comment

#288 - [WIP]284 update readme

Pull Request - State: open - Opened by nataliyah123 almost 5 years ago - 1 comment

#287 - Add section on running Jupyter notebooks

Pull Request - State: closed - Opened by mbonsma almost 6 years ago - 1 comment

#286 - Bac phage interactions

Pull Request - State: closed - Opened by mbonsma almost 6 years ago - 1 comment

#285 - Bac phage interactions

Pull Request - State: closed - Opened by mbonsma almost 6 years ago - 1 comment

#284 - Update README to include contributors section following 'All Contributors' guidelines

Issue - State: open - Opened by mbonsma over 6 years ago
Labels: good first issue, documentation

#283 - Issue #278 Add wait-retry function

Pull Request - State: closed - Opened by yuzhoux over 6 years ago - 2 comments

#282 - Beginnings of the pipeline to match spacers and phages

Pull Request - State: closed - Opened by mbonsma over 6 years ago - 1 comment

#281 - Correct file loading issue in repeats demo notebook

Pull Request - State: closed - Opened by aays over 6 years ago - 2 comments

#280 - Update demo notebooks to save images on AWS or in a different local / GitHub folder

Issue - State: open - Opened by mbonsma over 6 years ago
Labels: enhancement, question, code, mozsprint

#279 - Change to use heroku link and remove long print output

Pull Request - State: closed - Opened by mbonsma over 6 years ago - 1 comment

#278 - Add a wait function to the phaster demo notebook

Issue - State: open - Opened by mbonsma over 6 years ago - 2 comments
Labels: good first issue, code, mozsprint

#277 - try increasing pytest version to see if it fixes build issue

Pull Request - State: closed - Opened by mbonsma over 6 years ago - 1 comment

#276 - Make a separate requirements.txt for the demos folder

Issue - State: open - Opened by mbonsma over 6 years ago
Labels: help wanted, good first issue, documentation, mozsprint

#275 - Try out demo notebooks and report bugs / lack of documentation

Issue - State: open - Opened by mbonsma over 6 years ago - 3 comments
Labels: help wanted, good first issue, code, mozsprint

#274 - updated broken links.

Pull Request - State: closed - Opened by ghost over 6 years ago - 1 comment

#273 - updated broken links

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

#272 - Check links on README, fix or report broken ones

Issue - State: closed - Opened by mbonsma over 6 years ago - 2 comments
Labels: good first issue, documentation, mozsprint

#271 - Help wanted about how to find the relationship of phage-bacterium

Issue - State: closed - Opened by ghost over 6 years ago - 1 comment

#270 - Added repeat array class demo notebook

Pull Request - State: closed - Opened by aays over 6 years ago - 1 comment

#269 - added test case

Pull Request - State: closed - Opened by WxnChen11 over 6 years ago - 4 comments

#268 - Create test for entire organism addition pipeline

Issue - State: closed - Opened by mbonsma over 6 years ago - 1 comment

#267 - Code to add single organism to database at a time

Pull Request - State: closed - Opened by WxnChen11 over 6 years ago - 1 comment

#266 - Update README.md

Pull Request - State: closed - Opened by moijes12 over 6 years ago - 2 comments

#265 - Development environment setup scripts

Pull Request - State: closed - Opened by hallb almost 7 years ago - 1 comment

#264 - CRISPRfinder database - locus start and end positions wrong

Issue - State: open - Opened by mbonsma almost 7 years ago - 2 comments
Labels: bug, code

#263 - Change issue labels / make new ones that are more useful

Issue - State: open - Opened by mbonsma almost 7 years ago - 2 comments
Labels: help wanted, question, mozsprint

#262 - Data Pipeline Architecture Overview

Issue - State: open - Opened by patrick-wu almost 7 years ago - 1 comment
Labels: help wanted, question

#261 - Make smaller sample database for contributing

Issue - State: open - Opened by mbonsma almost 7 years ago
Labels: code, database

#260 - Subdivide into several repos

Issue - State: open - Opened by mbonsma almost 7 years ago - 4 comments
Labels: enhancement, help wanted, code

#259 - Research alternative algorithms for detecting CRISPR repeats and spacers

Issue - State: closed - Opened by mbonsma almost 7 years ago - 1 comment
Labels: help wanted, science

#258 - Edit installation section of README to better distinguish types of contributing / using

Issue - State: open - Opened by mbonsma almost 7 years ago - 1 comment
Labels: enhancement, documentation, code

#257 - Demo for working with the Phaster API

Pull Request - State: closed - Opened by mbonsma almost 7 years ago - 1 comment

#256 - Use Binder to host live demo notebooks?

Issue - State: open - Opened by mbonsma almost 7 years ago
Labels: code

#255 - Modifies collect accessions to download the ftp file

Pull Request - State: closed - Opened by cemyld almost 7 years ago

#254 - Search for putative Acr proteins

Issue - State: open - Opened by mbonsma almost 7 years ago
Labels: code, database

#253 - added R notebook for CRISPR type analysis

Pull Request - State: open - Opened by aays almost 7 years ago - 2 comments

#252 - Update extract_CRISPRdb.py to use local files instead of CRISPRdb website

Issue - State: open - Opened by mbonsma about 7 years ago - 2 comments
Labels: good first issue, code

#251 - PEP8 fixes

Pull Request - State: closed - Opened by delirious-lettuce about 7 years ago - 8 comments

#250 - Change crisprfinder.py to use perl script provided by creators

Issue - State: open - Opened by mbonsma about 7 years ago
Labels: code

#249 - Adds a list of organism ids that have confirmed active CRISPR systems.

Pull Request - State: closed - Opened by cemyld about 7 years ago

#248 - Attempted to fix #180

Pull Request - State: closed - Opened by shaniphankar about 7 years ago - 2 comments

#247 - Re-write to use pandas and add argument parsing

Pull Request - State: closed - Opened by thisisjaid about 7 years ago - 2 comments

#246 - Move numpy before biopython

Pull Request - State: closed - Opened by thisisjaid about 7 years ago - 1 comment

#245 - pip install -r fails on Ubuntu 16.04 w/ Python3

Issue - State: open - Opened by thisisjaid about 7 years ago - 2 comments

#244 - Remove hardcoded inputs and outputs in collect_accessions.py

Issue - State: closed - Opened by mbonsma about 7 years ago - 5 comments
Labels: good first issue, code

#243 - Scrape accessions from downloaded summary data

Pull Request - State: closed - Opened by mbonsma about 7 years ago - 8 comments

#242 - Loop through eukaryote genomes and run through CRISPRfinder

Issue - State: open - Opened by mbonsma about 7 years ago
Labels: code

#241 - eukaryote accession numbers

Pull Request - State: closed - Opened by mbonsma about 7 years ago - 1 comment

#240 - update crispr db link in crisprfinder script

Pull Request - State: closed - Opened by mbonsma over 7 years ago

#239 - crisprfinder script not working for some examples

Issue - State: open - Opened by mbonsma over 7 years ago - 8 comments
Labels: bug, code

#238 - Analysis: how do spacer loci correspond to cas gene cassettes?

Issue - State: open - Opened by mbonsma over 7 years ago
Labels: code, science

#237 - Additions to antiCRISPR and organism-antiCRISPR-pairs tables

Issue - State: open - Opened by mbonsma over 7 years ago
Labels: code, database

#236 - Add bacterial metadata to database

Issue - State: open - Opened by mbonsma over 7 years ago
Labels: code, database

#235 - Add prophage regions to chromosome visualization

Issue - State: open - Opened by mbonsma over 7 years ago
Labels: code

#234 - Look into how to use groupings of cas genes as signature of a genuine gene casette

Issue - State: open - Opened by mbonsma over 7 years ago
Labels: code

#233 - Specify number of mismatches for self-targeting spacers and use strict cutoff

Issue - State: open - Opened by mbonsma over 7 years ago
Labels: code, database

#232 - Implement length cutoff for cas gene matches to reduce spurious matches

Issue - State: open - Opened by mbonsma over 7 years ago
Labels: code, database

#231 - Notebook

Pull Request - State: closed - Opened by mbonsma over 7 years ago - 1 comment

#230 - Adds initial script for blasting self targeting spacers

Pull Request - State: closed - Opened by cemyld over 7 years ago - 1 comment

#229 - Wanted: front-end developer to help us plan (and build) a front-end!

Issue - State: open - Opened by mbonsma over 7 years ago - 4 comments
Labels: help wanted, question, front end, web

#222 - change format of outfmt argument to fix error and add example usage

Pull Request - State: closed - Opened by mbonsma over 7 years ago - 2 comments

#219 - Update README with new usage now that we have a database

Issue - State: closed - Opened by mbonsma over 7 years ago - 1 comment
Labels: documentation

#210 - delete profile_dict function and fix data file path

Pull Request - State: closed - Opened by mbonsma over 7 years ago

#209 - Updates bac_accession_list to the most recent DRdatabase file.

Pull Request - State: closed - Opened by cemyld over 7 years ago

#208 - update DRdatabase and spacerdatabase files from CRISPRdb website

Pull Request - State: closed - Opened by mbonsma over 7 years ago

#207 - Twelve Factor Compatibility

Pull Request - State: closed - Opened by cemyld over 7 years ago

#206 - Restructuring root directory

Pull Request - State: closed - Opened by cemyld over 7 years ago - 1 comment

#205 - Modifies the field constraints and changes evalue to float.

Pull Request - State: closed - Opened by cemyld over 7 years ago

#202 - sort spacer dictionary so order is in order

Pull Request - State: closed - Opened by mbonsma over 7 years ago

#199 - Figure out what exactly we should be downloading from NCBI in terms of bacterial and archaeal genomes

Issue - State: closed - Opened by mbonsma over 7 years ago - 13 comments
Labels: help wanted, good first issue, science

#196 - Update bac_accession_list with all NCBI microbes

Issue - State: closed - Opened by mbonsma over 7 years ago - 3 comments
Labels: documentation, science

#193 - Script to populate OrganismCasPair and CasProtein tables, cas profiles from Makarova et al

Pull Request - State: closed - Opened by mbonsma over 7 years ago

#191 - Make everything follow PEP8

Issue - State: open - Opened by QuLogic over 7 years ago - 6 comments
Labels: enhancement, help wanted, documentation, code

#188 - Update the dbschema diagram with newer models.

Pull Request - State: closed - Opened by cemyld over 7 years ago

#187 - Add casprotein model and update endpoints

Pull Request - State: closed - Opened by cemyld over 7 years ago - 1 comment

#185 - Renames models file to phage.py

Pull Request - State: closed - Opened by cemyld over 7 years ago

#180 - Delete (?) Usage section from README until we can update it

Issue - State: closed - Opened by mbonsma over 7 years ago - 2 comments
Labels: good first issue, documentation

#178 - New database schema

Pull Request - State: closed - Opened by cemyld over 7 years ago

#173 - Merge from master

Pull Request - State: closed - Opened by cemyld over 7 years ago

#172 - Adding Travis-CI support for Django testing

Pull Request - State: closed - Opened by cemyld over 7 years ago - 2 comments

#169 - Move fetch and fix regex error

Pull Request - State: closed - Opened by cemyld over 7 years ago

#167 - add link to Firefox SQLite manager plugin

Pull Request - State: closed - Opened by mbonsma over 7 years ago

#163 - Installation in Readme

Pull Request - State: closed - Opened by cemyld over 7 years ago

#161 - Adds an initial requirements.txt file for pip installing dependencies.

Pull Request - State: closed - Opened by cemyld over 7 years ago

#149 - Script to determine CRISPR type from cas genes

Issue - State: open - Opened by mbonsma over 7 years ago - 4 comments
Labels: code, database

#144 - Gitignore python

Pull Request - State: closed - Opened by cemyld over 7 years ago - 1 comment

#143 - Filechecker and downloader

Pull Request - State: closed - Opened by cemyld over 7 years ago - 4 comments

#142 - Analysis: distribution of CRISPR loci sizes

Issue - State: closed - Opened by mbonsma over 7 years ago - 4 comments
Labels: code, science, database

#141 - Join us at the Mozilla Global Sprint, June 1-2!

Issue - State: closed - Opened by mbonsma over 7 years ago
Labels: help wanted

#139 - Create script to populate database with organism/antiCRISPR pairs

Issue - State: closed - Opened by mbonsma over 7 years ago - 2 comments
Labels: code, database

#138 - Data type mismatch when running database migrations

Issue - State: closed - Opened by mbonsma over 7 years ago - 7 comments
Labels: bug, code

#134 - Make phageParser logo!

Issue - State: closed - Opened by mbonsma over 7 years ago - 6 comments
Labels: help wanted, good first issue, science

#129 - CRISPR type decision table

Pull Request - State: closed - Opened by mbonsma over 7 years ago

#128 - Removes unused code from models.py

Pull Request - State: closed - Opened by cemyld over 7 years ago - 1 comment

#125 - Created a script to populate Organism model in Django app

Pull Request - State: closed - Opened by cemyld over 7 years ago - 1 comment

#122 - Populate database with antiCRISPR accessions and sequences

Issue - State: closed - Opened by mbonsma over 7 years ago - 1 comment
Labels: good first issue, code, database

#121 - Add text file with accession numbers for phage antiCRISPR genes

Pull Request - State: closed - Opened by mbonsma over 7 years ago

#112 - Roadmap

Issue - State: open - Opened by mbonsma over 7 years ago

#29 - Convert phage identifier headers into phage names

Issue - State: closed - Opened by mbonsma over 9 years ago - 10 comments
Labels: good first issue, code

GitHub / phageParser/phageParser issues and pull requests