Ecosyste.ms: Issues

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

GitHub / medema-group/bigslice issues and pull requests

#92 - antismash version compatibility issues

Issue - State: open - Opened by CRZ0128 18 days ago

#91 - Can't find a matching hmm library in the database!

Issue - State: open - Opened by 1362996609zby 2 months ago - 6 comments

#90 - Output folder didn't exists when I was running query mode

Issue - State: closed - Opened by 1362996609zby 2 months ago - 1 comment

#89 - BGC Taxonomy table empty

Issue - State: open - Opened by intikhab 2 months ago

#87 - KeyError: '[6680] not in index'

Issue - State: closed - Opened by ZhangDengwei 4 months ago - 2 comments

#86 - Bugfix: Explicitly use "amino" alphabet when reading in CDS multifasta

Pull Request - State: closed - Opened by dtdoering 4 months ago - 5 comments

#85 - Update __init__.py

Pull Request - State: closed - Opened by dtdoering 4 months ago

#84 - Update fetch_taxonomy_from_api.py for updated GTDB API

Pull Request - State: closed - Opened by dtdoering 5 months ago

#83 - Are antismash versions important?

Issue - State: open - Opened by ayaloglu 8 months ago - 3 comments

#82 - ValueError: Could not determine alphabet of file

Issue - State: closed - Opened by yuezhiTang 9 months ago - 7 comments

#80 - Problems encountered while running bigslice

Issue - State: closed - Opened by yuezhiTang 9 months ago

#77 - antismash version7 output not recognized by bigslice

Issue - State: closed - Opened by HongjaePark86 about 1 year ago - 2 comments

#75 - antiSMASH output .gbk files not recognized by BigSlice

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

#74 - "is not a recognized antiSMASH clustergbk"

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

#72 - How do I extract similar BGC distance values from the interactive output

Issue - State: open - Opened by boykawang over 1 year ago - 18 comments

#71 - Fetching the download_bigslice_hmmdb

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

#70 - datasets.tsv

Issue - State: open - Opened by wang123yue over 1 year ago

#69 - Improved code

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

#68 - KeyError while running bigslice

Issue - State: closed - Opened by AmayAgrawal over 1 year ago - 5 comments

#65 - Installation check

Issue - State: open - Opened by yschencau almost 2 years ago - 6 comments

#64 - Update generate_antismash_gbk.py

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

#63 - Running on a job queue / non-interactive environment

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

#62 - Update .gitignore, changed Python logging, added exception handling.

Pull Request - State: closed - Opened by louwersj about 2 years ago - 5 comments

#61 - Issue Querying antiSMASH BGCs

Issue - State: open - Opened by planctoqueen about 2 years ago - 5 comments

#60 - CVE-2007-4559 Patch

Pull Request - State: closed - Opened by TrellixVulnTeam about 2 years ago

#59 - Parsing and Inserting gbks from MIBiG

Issue - State: open - Opened by nicholascdove about 2 years ago - 5 comments

#58 - Incorrect version

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

#57 - extract_bgcs_metadata.py AttributeError

Issue - State: closed - Opened by neptuneyt about 2 years ago - 11 comments

#56 - Cosine distance among BGCs

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

#55 - Changing the default temporary directory location

Issue - State: open - Opened by matinnuhamunada over 2 years ago

#54 - where the Can't find HMM model libraries can be put ?

Issue - State: closed - Opened by Caiyulu-818 over 2 years ago - 2 comments

#53 - must using antismash parameter --pfam2go?

Issue - State: open - Opened by Caiyulu-818 over 2 years ago

#52 - Suggestion: remove interactive prompts

Issue - State: open - Opened by danudwary over 2 years ago

#51 - os.sched_getaffinity not available on MacOS

Issue - State: open - Opened by danudwary over 2 years ago

#50 - bigslice output

Issue - State: open - Opened by INFINITY1993 over 2 years ago - 2 comments

#48 - BiG-SLiCE output visualization issues: jsonify'd DataTables & antiSMASH6

Issue - State: open - Opened by ialas almost 3 years ago - 2 comments

#47 - Trouble querying antiSMASH BGCs

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

#46 - Broken link for jupyter notebook scripts?

Issue - State: open - Opened by matinnuhamunada almost 3 years ago - 1 comment

#45 - Unpack error

Issue - State: closed - Opened by kpenn88 about 3 years ago - 5 comments

#44 - Possible to generate a data frame output from Interactive output

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

#43 - question about input folder (clustering mode)

Issue - State: closed - Opened by Valentin-Bio-zz over 3 years ago - 1 comment

#42 - can't use pip install ./bigslice/ commend

Issue - State: open - Opened by byeollee over 3 years ago - 2 comments

#41 - [Question] Pre-processed antiSMASH results from BiG-SLiCE paper

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

#40 - [Question]: isolate_fungal dataset in pre-processed dataset

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

#38 - using with gecco

Issue - State: closed - Opened by smb20200615 over 3 years ago

#37 - raise FileNotFoundError() while pharsing hmmtext

Issue - State: open - Opened by ZehanDai almost 4 years ago - 2 comments

#36 - bug: parsed folder paths lose its first letter

Issue - State: closed - Opened by satriaphd almost 4 years ago

#35 - antiSMASH 6

Issue - State: open - Opened by satriaphd almost 4 years ago - 1 comment

#34 - Error when generating antismash-like reions

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

#33 - Missing script for taxonomy assignment

Issue - State: closed - Opened by artur-matysik almost 4 years ago - 3 comments

#32 - start_server.sh fails on macOS

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

#31 - Failure to run example input folder

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

#30 - Select cpus from os.sched_getaffinity()

Pull Request - State: closed - Opened by waltersom about 4 years ago - 2 comments

#29 - Add BiG-SLiCE to Bioconda

Issue - State: open - Opened by mdehollander about 4 years ago

#28 - Add a conda environment file

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

#27 - Error: download_bigslice_hmmdb

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

#26 - fix #24 type in readme

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

#25 - Can't find preprocessed data from NCBI BGCs

Issue - State: closed - Opened by valntn over 4 years ago - 1 comment

#24 - typo in readme

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

#23 - Missing link in README

Issue - State: closed - Opened by chasemc over 4 years ago - 1 comment

#22 - overlapping antiSMASH domains

Issue - State: open - Opened by satriaphd over 4 years ago
Labels: enhancement

#21 - minor readme edit

Pull Request - State: closed - Opened by chevrm over 4 years ago - 3 comments

#20 - Link to taxonomy assignment script broken?

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

#19 - [!] algorithm improvement (note to all users!)

Issue - State: open - Opened by satriaphd over 4 years ago - 3 comments

#18 - Link to preprocessed NCBI database broken

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

#17 - idea: BGC (local) alignments

Issue - State: open - Opened by satriaphd over 4 years ago
Labels: enhancement

#16 - style: refactor main script

Issue - State: open - Opened by satriaphd over 4 years ago
Labels: enhancement

#15 - core: store (subpfam) hsp -> (biosyn_pfam) hsp relationship

Issue - State: closed - Opened by satriaphd over 4 years ago - 1 comment

#14 - Optimize the runtimes of subpfam scanning

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

#13 - idea: constructing CORASON-like phylogeny

Issue - State: open - Opened by satriaphd almost 5 years ago
Labels: enhancement

#12 - Explore MMseq2 for subpfam scan

Issue - State: open - Opened by satriaphd almost 5 years ago
Labels: enhancement

#11 - incorporate nucleotide sequences of BGCs

Issue - State: open - Opened by satriaphd almost 5 years ago

#10 - method: implements redundancy filtering prior to k-means

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

#9 - method: use hmmsearch instead of hmmscan

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

#8 - method: use hmm-scanned/searched alignments to RP15 database

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

#7 - milestone: implements an interactive (local)web output

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

#6 - milestone: implements K-means clustering of features

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

#5 - milestone: implements feature extraction

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

#4 - feature: enable whole system profiling

Issue - State: open - Opened by satriaphd about 5 years ago
Labels: enhancement

#3 - improvement: tidy but informative print outputs

Issue - State: open - Opened by satriaphd about 5 years ago
Labels: enhancement

#2 - method: include (pl)antiSMASH HMMs as features

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

#1 - request: please enable separating input BGCs into datasets

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