biocore/micronota issues and pull requests

#84 - Some Questions about q2-fragment-insertion

Issue - State: open - Opened by cafferychen777 about 2 years ago

#83 - refactor xml parser to reduce memory footprint

Pull Request - State: open - Opened by RNAer almost 7 years ago - 1 comment

#82 - ENH: antimicrobial and virulence genes identification

Issue - State: open - Opened by tkosciol almost 7 years ago

#81 - update README and add conda build recipe

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

#80 - update with snakemake

Pull Request - State: closed - Opened by RNAer about 7 years ago - 3 comments

#79 - use snakemake and IntervalMetadata

Pull Request - State: closed - Opened by RNAer about 8 years ago - 6 comments

#78 - use snakemake and IntervalMetadata

Pull Request - State: closed - Opened by RNAer about 8 years ago - 5 comments

#77 - Updating parsers

Issue - State: open - Opened by mortonjt about 8 years ago

#76 - Transport proteins

Issue - State: open - Opened by mortonjt over 8 years ago
Labels: features to annotate

#75 - migrate from burrito to dumpling

Pull Request - State: closed - Opened by RNAer over 8 years ago - 7 comments

#74 - Parser cmscan

Pull Request - State: closed - Opened by sjanssen2 over 8 years ago - 4 comments

#73 - Failed building wheel for scipy

Issue - State: closed - Opened by sjanssen2 over 8 years ago - 2 comments

#72 - use sam parser for diamond output

Pull Request - State: closed - Opened by RNAer over 8 years ago - 2 comments

#71 - Cache fix

Pull Request - State: closed - Opened by mortonjt over 8 years ago - 5 comments

#70 - GFF format parser and tests

Pull Request - State: open - Opened by tkosciol over 8 years ago - 10 comments

#69 - Add option to create database of functional assignments

Issue - State: open - Opened by elsherbini over 8 years ago - 1 comment

#68 - FIX: sam parser empty case

Pull Request - State: closed - Opened by mortonjt over 8 years ago - 2 comments

#67 - get aligned length from diamond SAM output

Issue - State: open - Opened by RNAer over 8 years ago - 1 comment

#66 - misc changes

Pull Request - State: closed - Opened by RNAer over 8 years ago - 3 comments

#65 - SAM parser sniffer warning

Issue - State: open - Opened by RNAer over 8 years ago - 2 comments

#64 - Cache

Pull Request - State: closed - Opened by mortonjt over 8 years ago - 4 comments

#63 - Store CIGAR strings from Diamond alignment

Issue - State: open - Opened by mortonjt over 8 years ago

#62 - ENH: Skeleton code for Config file

Pull Request - State: closed - Opened by souravsingh over 8 years ago - 2 comments

#61 - signalP integration

Pull Request - State: open - Opened by tkosciol over 8 years ago - 6 comments

#60 - FIX: Fixed parsing sam output

Pull Request - State: closed - Opened by mortonjt over 8 years ago

#59 - WIP : Cache

Pull Request - State: closed - Opened by mortonjt over 8 years ago

#58 - ENH: Adding in sam parsers

Pull Request - State: closed - Opened by mortonjt over 8 years ago

#57 - Abstracting out File IO

Issue - State: open - Opened by mortonjt over 8 years ago
Labels: question

#56 - SAM parser

Pull Request - State: closed - Opened by mortonjt over 8 years ago - 4 comments

#55 - time benchmark

Issue - State: open - Opened by RNAer over 8 years ago

#55 - time benchmark

Issue - State: open - Opened by RNAer over 8 years ago

#54 - configuration and logging

Pull Request - State: closed - Opened by RNAer over 8 years ago - 8 comments

#53 - IO parsers for GFF

Issue - State: open - Opened by tkosciol over 8 years ago - 3 comments
Labels: on deck

#52 - SAM/BAM parsers

Issue - State: closed - Opened by mortonjt over 8 years ago - 1 comment
Labels: on deck

#51 - MinCED wrapper

Pull Request - State: closed - Opened by tkosciol over 8 years ago - 6 comments

#50 - add dry run option

Issue - State: open - Opened by RNAer over 8 years ago
Labels: on deck

#49 - set checkpoint

Issue - State: open - Opened by RNAer over 8 years ago
Labels: on deck

#48 - refactoring the functions in each bfillings

Issue - State: closed - Opened by RNAer over 8 years ago
Labels: on deck

#47 - add logging to log running info

Issue - State: open - Opened by RNAer over 8 years ago
Labels: on deck

#46 - WIP: final pr before alpha release

Pull Request - State: closed - Opened by RNAer over 8 years ago - 1 comment

#45 - Configuration file

Issue - State: open - Opened by mortonjt almost 9 years ago - 2 comments
Labels: help wanted, quick fix

#44 - fine touch on tigrfam and uniref

Pull Request - State: closed - Opened by RNAer almost 9 years ago - 2 comments

#43 - WIP: big change

Pull Request - State: closed - Opened by RNAer almost 9 years ago - 4 comments

#42 - Add config parser

Pull Request - State: closed - Opened by RNAer almost 9 years ago - 1 comment

#41 - WIP: New Sequence data structure

Pull Request - State: closed - Opened by mortonjt almost 9 years ago

#40 - database framework and tigrfam

Pull Request - State: closed - Opened by RNAer almost 9 years ago - 12 comments

#39 - databases for functional assignment

Issue - State: open - Opened by RNAer almost 9 years ago - 1 comment

#38 - gene calling tools

Issue - State: open - Opened by RNAer almost 9 years ago
Labels: features to annotate

#37 - Update Makefile and other files accordingly

Pull Request - State: closed - Opened by RNAer almost 9 years ago - 7 comments

#36 - Minor fix for sphinx setup

Pull Request - State: closed - Opened by RNAer almost 9 years ago

#35 - Revert "setup sphinx doc"

Pull Request - State: closed - Opened by mortonjt almost 9 years ago

#34 - autocomplete.sh

Issue - State: open - Opened by mortonjt almost 9 years ago - 4 comments
Labels: question, quick fix

#33 - Add the script for cmd line Tab completion

Pull Request - State: closed - Opened by RNAer almost 9 years ago - 3 comments

#32 - setup sphinx doc

Pull Request - State: closed - Opened by RNAer almost 9 years ago - 7 comments

#31 - add sphinx documentation

Issue - State: closed - Opened by RNAer almost 9 years ago
Labels: on deck, documentation

#30 - biosynthetic gene cluster annotation

Issue - State: open - Opened by mortonjt about 9 years ago - 1 comment
Labels: features to annotate

#29 - Finish Diamond wrapper

Pull Request - State: closed - Opened by RNAer about 9 years ago - 3 comments

#28 - improve .travis.yml

Pull Request - State: closed - Opened by RNAer about 9 years ago - 6 comments

#27 - Hmmbase

Pull Request - State: closed - Opened by mortonjt about 9 years ago - 4 comments

#26 - Creating base class for HMMER and Infernal

Issue - State: closed - Opened by mortonjt about 9 years ago
Labels: on deck

#25 - misc changes on repo setup

Pull Request - State: closed - Opened by RNAer about 9 years ago

#24 - Improve travis CI

Issue - State: closed - Opened by RNAer about 9 years ago
Labels: quick fix, on deck

#23 - Add licenses for each tool and database we use

Issue - State: closed - Opened by RNAer about 9 years ago
Labels: quick fix, on deck

#22 - Reorganizing Prodigal test files

Pull Request - State: closed - Opened by mortonjt about 9 years ago - 1 comment

#21 - Infernal wrapper

Pull Request - State: closed - Opened by RNAer about 9 years ago - 4 comments

#20 - Add Aragorn wrapper for tRNA/tmRNA prediction

Issue - State: open - Opened by RNAer about 9 years ago
Labels: on deck, features to annotate

#19 - antibiotic resistance gene annotation

Issue - State: open - Opened by RNAer about 9 years ago
Labels: features to annotate

#18 - Add SignalP for signal peptide prediction

Issue - State: open - Opened by RNAer about 9 years ago - 3 comments
Labels: on deck, features to annotate

#17 - Add MinCED for CRIPSR prediction

Issue - State: open - Opened by RNAer about 9 years ago - 2 comments
Labels: on deck, features to annotate

#16 - virulence factor annotation

Issue - State: open - Opened by RNAer about 9 years ago - 2 comments
Labels: features to annotate

#15 - promoter prediction

Issue - State: open - Opened by RNAer about 9 years ago
Labels: features to annotate

#14 - protease predictions

Issue - State: open - Opened by RNAer about 9 years ago
Labels: features to annotate

#13 - annotate carbohydrate active enzymes

Issue - State: open - Opened by RNAer about 9 years ago - 1 comment
Labels: features to annotate

#12 - Add contributing guidelines

Pull Request - State: closed - Opened by RNAer about 9 years ago - 2 comments

#11 - add contribution guide line

Issue - State: closed - Opened by RNAer about 9 years ago

#10 - Needs API documentation

Issue - State: closed - Opened by RNAer about 9 years ago - 2 comments
Labels: documentation

#9 - Replace my own branch with biocore's

Pull Request - State: closed - Opened by RNAer about 9 years ago

#8 - Needs a CHANGELOG

Issue - State: closed - Opened by mortonjt about 9 years ago
Labels: documentation

#7 - add infernal and HMMer wrappers

Issue - State: closed - Opened by RNAer about 9 years ago - 13 comments
Labels: help wanted

#6 - add Diamond wrapper

Issue - State: closed - Opened by RNAer about 9 years ago
Labels: help wanted

#5 - Add travis and coverall integration

Pull Request - State: closed - Opened by RNAer about 9 years ago - 5 comments

#4 - prodigal wrapper

Pull Request - State: closed - Opened by RNAer about 9 years ago - 6 comments

#3 - make it conda installable

Issue - State: closed - Opened by RNAer about 9 years ago - 14 comments
Labels: help wanted

#2 - Initiation

Pull Request - State: closed - Opened by RNAer about 9 years ago - 6 comments

#1 - command line interface

Issue - State: open - Opened by RNAer about 9 years ago - 3 comments
Labels: help wanted, question

GitHub / biocore/micronota issues and pull requests