medema-group/bigslice issues and pull requests

#98 - how can I get the Novelty of BGCs

Issue - State: open - Opened by yr1997yr 4 months ago

#97 - output_tsv issue

Issue - State: open - Opened by XingshuaiCui 4 months ago

#96 - KeyError: 'hmm_id'

Issue - State: closed - Opened by coderachal 5 months ago

#95 - output-tsv fails

Issue - State: open - Opened by chasemc 7 months ago

#94 - Output folder didn't exists!

Issue - State: closed - Opened by CynthiaBecker 7 months ago - 1 comment

#93 - AttributeError: 'pyhmmer.plan7.TopHits' object has no attribute 'query_accession'

Issue - State: open - Opened by 123xiaochen 8 months ago

#92 - antismash version compatibility issues

Issue - State: open - Opened by CRZ0128 8 months ago

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

Issue - State: open - Opened by 1362996609zby 9 months ago

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

Issue - State: closed - Opened by 1362996609zby 9 months ago - 1 comment

#89 - BGC Taxonomy table empty

Issue - State: open - Opened by intikhab 10 months ago

#88 - Use sqlite3 builtin database `backup()` to avoid query string size limit

Pull Request - State: open - Opened by dtdoering 11 months ago

#88 - Use sqlite3 builtin database `backup()` to avoid query string size limit

Pull Request - State: closed - Opened by dtdoering 11 months ago

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

Issue - State: closed - Opened by ZhangDengwei 11 months ago - 2 comments

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

Pull Request - State: closed - Opened by dtdoering 11 months ago - 5 comments

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

Pull Request - State: open - Opened by dtdoering 11 months ago

#85 - Update init.py

Pull Request - State: closed - Opened by dtdoering 11 months ago

#85 - Update init.py

Pull Request - State: closed - Opened by dtdoering 11 months ago

#84 - Update fetch_taxonomy_from_api.py for updated GTDB API

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

#84 - Update fetch_taxonomy_from_api.py for updated GTDB API

Pull Request - State: open - Opened by dtdoering 12 months ago

#83 - Are antismash versions important?

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

#82 - ValueError: Could not determine alphabet of file

Issue - State: closed - Opened by yuezhiTang over 1 year ago - 7 comments

#81 - “sqlite3.OperationalError: unable to open database file” error when using "--export-tsv"

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

#80 - Problems encountered while running bigslice

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

#79 - Add Option to Disable L2-Normalization for Compatibility with Older BiG-SLICE Results

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

#77 - antismash version7 output not recognized by bigslice

Issue - State: closed - Opened by HongjaePark86 almost 2 years ago - 2 comments

#76 - BGCs are being clustered into one GCF, and the distance values appear identical.

Issue - State: open - Opened by ChrisC610 almost 2 years ago

#74 - "is not a recognized antiSMASH clustergbk"

Issue - State: closed - Opened by MingyueCheng almost 2 years ago

#73 - Remove the BGC id's which does not have any features extracted before performing the final clustering

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

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

Issue - State: open - Opened by boykawang about 2 years ago - 18 comments

#71 - Fetching the download_bigslice_hmmdb

Issue - State: closed - Opened by MenusGarg about 2 years ago

#70 - datasets.tsv

Issue - State: open - Opened by wang123yue about 2 years ago

#69 - Improved code

Pull Request - State: closed - Opened by louwersj over 2 years ago

#68 - KeyError while running bigslice

Issue - State: closed - Opened by AmayAgrawal over 2 years ago - 5 comments

#67 - "Can't find a matching hmm library in the database!" when running --query mode from antiSMASH v6 results

Issue - State: open - Opened by jolespin over 2 years ago - 10 comments

#66 - [Feature Request] Remove the requirement for the output directory to have a subdirectory called `result` (even in a new run)

Issue - State: open - Opened by jolespin over 2 years ago - 1 comment

#65 - Installation check

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

#64 - Update generate_antismash_gbk.py

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

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

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

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

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

#61 - Issue Querying antiSMASH BGCs

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

#60 - CVE-2007-4559 Patch

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

#59 - Parsing and Inserting gbks from MIBiG

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

#58 - Incorrect version

Issue - State: open - Opened by dalwindercheema almost 3 years ago

#57 - extract_bgcs_metadata.py AttributeError

Issue - State: closed - Opened by neptuneyt almost 3 years ago - 11 comments

#56 - Cosine distance among BGCs

Issue - State: open - Opened by neptuneyt almost 3 years ago

#55 - Changing the default temporary directory location

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

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

Issue - State: closed - Opened by Caiyulu-818 about 3 years ago - 2 comments

#53 - must using antismash parameter --pfam2go?

Issue - State: open - Opened by Caiyulu-818 about 3 years ago

#52 - Suggestion: remove interactive prompts

Issue - State: open - Opened by danudwary about 3 years ago

#51 - os.sched_getaffinity not available on MacOS

Issue - State: open - Opened by danudwary about 3 years ago

#50 - bigslice output

Issue - State: open - Opened by INFINITY1993 about 3 years ago - 2 comments

#49 - Error in generation of antismash regions using "generate_antismash_gbk.py"

Issue - State: open - Opened by mfrand-7 over 3 years ago

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

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

#47 - Trouble querying antiSMASH BGCs

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

#46 - Broken link for jupyter notebook scripts?

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

#45 - Unpack error

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

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

Issue - State: closed - Opened by ashwinssudarshan almost 4 years ago - 1 comment

#43 - question about input folder (clustering mode)

Issue - State: closed - Opened by Valentin-Bio-zz almost 4 years ago - 1 comment

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

Issue - State: open - Opened by byeollee about 4 years ago - 2 comments

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

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

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

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

#39 - Cases when the taxonomy information of the interested species is only partially available

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

#38 - using with gecco

Issue - State: closed - Opened by smb20200615 over 4 years ago

#37 - raise FileNotFoundError() while pharsing hmmtext

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

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

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

#35 - antiSMASH 6

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

#34 - Error when generating antismash-like reions

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

#33 - Missing script for taxonomy assignment

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

#31 - Failure to run example input folder

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

#30 - Select cpus from os.sched_getaffinity()

Pull Request - State: closed - Opened by waltersom almost 5 years ago - 2 comments

#29 - Add BiG-SLiCE to Bioconda

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

#28 - Add a conda environment file

Pull Request - State: closed - Opened by mdehollander almost 5 years ago - 1 comment

#27 - Error: download_bigslice_hmmdb

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

#26 - fix #24 type in readme

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

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

Issue - State: closed - Opened by valntn almost 5 years ago - 1 comment

#24 - typo in readme

Issue - State: closed - Opened by snayfach almost 5 years ago

#23 - Missing link in README

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

#22 - overlapping antiSMASH domains

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

#21 - minor readme edit

Pull Request - State: closed - Opened by chevrm about 5 years ago - 3 comments

#20 - Link to taxonomy assignment script broken?

Issue - State: closed - Opened by tamuanand about 5 years ago - 2 comments

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

Issue - State: open - Opened by satriaphd about 5 years ago - 3 comments

#18 - Link to preprocessed NCBI database broken

Issue - State: closed - Opened by bjreisman about 5 years ago - 2 comments

#17 - idea: BGC (local) alignments

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

#16 - style: refactor main script

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

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

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

#14 - Optimize the runtimes of subpfam scanning

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

#13 - idea: constructing CORASON-like phylogeny

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

#12 - Explore MMseq2 for subpfam scan

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