Ecosyste.ms: Issues

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GitHub / gamcil/cblaster issues and pull requests

#107 - error with extract_clusters

Issue - State: open - Opened by corkdagga 21 days ago - 1 comment

#106 - Update CITATION.cff with paper DOI

Pull Request - State: closed - Opened by althonos 3 months ago - 2 comments

#105 - An auxiliary script that migt help

Issue - State: open - Opened by AhmedElsherbini 3 months ago

#104 - OSError: Unable to parse NCBI response

Issue - State: open - Opened by GaoSpark 6 months ago - 3 comments

#103 - clinker plot_cluster legend issue

Issue - State: open - Opened by MarcosVoutsinos 6 months ago

#102 - Searching genomes without gene predictions

Issue - State: open - Opened by kcamnairb 9 months ago

#99 - "zsh: illegal hardware instruction" error

Issue - State: open - Opened by andtrum 11 months ago - 3 comments

#98 - cblaster remote error with large clusters

Issue - State: open - Opened by HackenDirker 12 months ago - 1 comment

#97 - extract_clusters shifting reading frame

Issue - State: open - Opened by McClenagoat about 1 year ago

#96 - AttributeError: 'NoneType' object has no attribute 'group'

Issue - State: open - Opened by yye88 about 1 year ago - 4 comments

#95 - Tree plot with 5 hits maximun per specie

Issue - State: open - Opened by Alvarosmb about 1 year ago

#93 - makedb from gbk files

Issue - State: open - Opened by Tim-Kirkwood over 1 year ago

#91 - cblaster didn't create .dmnd out file???????

Issue - State: open - Opened by neelam19051 over 1 year ago - 7 comments

#90 - TypeError: unsupported format string passed to NoneType.__format__

Issue - State: closed - Opened by yye88 over 1 year ago - 5 comments

#89 - makedb always results in 'sqlite3.OperationalError: database is locked'

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

#88 - Saving session JSON from GUI

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

#87 - Extra logging and hmmsearch fix

Pull Request - State: closed - Opened by malanjary-wur over 1 year ago - 4 comments

#86 - Fix off-by-one error when using extract_clusters module

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

#85 - problem with context.py

Issue - State: open - Opened by orlowskamga over 1 year ago - 9 comments

#84 - Error during "Fetching genomic context"

Issue - State: closed - Opened by Adwaith99 over 1 year ago - 5 comments

#83 - extract_clusters off by a bp

Issue - State: closed - Opened by galacmr over 1 year ago - 10 comments

#82 - illegal hardware instruction cblaster error

Issue - State: closed - Opened by Pacca97 almost 2 years ago

#81 - Error using makedb with gff and fa files

Issue - State: open - Opened by Rene-Hoover almost 2 years ago - 5 comments

#80 - not able to proceed with gne and clinker

Issue - State: open - Opened by pksun1 about 2 years ago - 3 comments

#79 - Issues with sqlite3 and initiating cblaster

Issue - State: open - Opened by pksun1 about 2 years ago - 2 comments

#78 - IndexError fix when no hits are found in a scaffold

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

#77 - Bug fixes, code enhancements, and file compression

Pull Request - State: closed - Opened by brymerr921 about 2 years ago - 1 comment

#76 - Local runs fail with `-bat identity -bkey max`

Issue - State: closed - Opened by chasemc over 2 years ago - 1 comment

#75 - Detection of Hits not perfect

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

#74 - cblaster makedb: error: argument paths: Invalid path:

Issue - State: closed - Opened by JordanVV over 2 years ago - 1 comment

#73 - Finding 1 pfam in metagenome

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

#72 - Error encode in database create.

Issue - State: open - Opened by Maiya19724 over 2 years ago - 1 comment

#70 - How do I avoid RecursionError?

Issue - State: open - Opened by robin84tk over 2 years ago - 2 comments

#69 - How to plot output after using "hmm" mode?

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

#68 - low sensitibity using local search mode

Issue - State: closed - Opened by yye88 over 2 years ago - 4 comments

#67 - database building error

Issue - State: open - Opened by yye88 over 2 years ago - 4 comments

#66 - No route to host

Issue - State: open - Opened by yye88 over 2 years ago

#65 - installation looking for wheel

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

#64 - Red and orange borders in heat map

Issue - State: closed - Opened by aberaslop almost 3 years ago - 2 comments

#63 - makedb issue

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

#62 - error

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

#61 - Extract issu

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

#60 - ValueError: not enough values to unpack (expected 2, got 0)

Issue - State: closed - Opened by lydia1201 almost 3 years ago - 1 comment

#59 - Allow local profile HMMs

Pull Request - State: closed - Opened by gamcil almost 3 years ago

#58 - The sequence length affects the final result

Issue - State: open - Opened by zuoyang97 almost 3 years ago

#57 - No configuration folder detected, please run cblaster config

Issue - State: closed - Opened by zuoyang97 almost 3 years ago - 4 comments

#56 - extract -ig hits?

Issue - State: open - Opened by mafeeney about 3 years ago - 1 comment

#55 - extract error -de expected one argument

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

#54 - ValueError: not enough values to unpack (expected 2, got 0)

Issue - State: closed - Opened by camilogarciabotero about 3 years ago - 7 comments

#53 - LONG TIME

Issue - State: closed - Opened by zuoyang97 about 3 years ago - 9 comments

#52 - invalid Entrez search term

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

#51 - No e-mail or NCBI API key found

Issue - State: closed - Opened by sschrstn about 3 years ago - 1 comment

#50 - Updated windows executable

Pull Request - State: closed - Opened by LianaGrieken about 3 years ago

#49 - Fix tests

Pull Request - State: closed - Opened by gamcil about 3 years ago

#48 - Save query cluster inside cblaster session

Pull Request - State: closed - Opened by gamcil about 3 years ago

#47 - small fix for python 3.6

Pull Request - State: closed - Opened by bramvanwersch about 3 years ago

#46 - Hmm improvements

Pull Request - State: closed - Opened by gamcil about 3 years ago

#45 - Windows/Mac executables, -per/--percentage option

Pull Request - State: closed - Opened by gamcil about 3 years ago

#44 - Add config module

Pull Request - State: closed - Opened by gamcil about 3 years ago

#43 - Executable Windows & bug fixes

Pull Request - State: closed - Opened by LianaGrieken about 3 years ago

#42 - Fix help menus

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

#41 - fixed windows test to include new genes that are returned by ncbi

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

#40 - Unable to make database. genome_parser function returning empty list.

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

#39 - GUI horizontal box not large enough for text

Issue - State: closed - Opened by StefaanVerwimp over 3 years ago - 2 comments

#38 - change list to tuple for button color to prevent errors

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

#37 - parse all locations for each feature, so module works for euk genomes

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

#36 - Fix linux tests

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

#35 - Test fixes

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

#34 - Intergaration tests

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

#33 - Minor bug fixes

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

#32 - genome_parsers test suite + some refactoring

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

#31 - Classes tests

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

#30 - Clinker int changes

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

#29 - Formatting

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

#28 - Improved integration tests

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

#27 - Fix databases remote

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

#26 - remove empty rows when hiding columns

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

#25 - Max cluster plot change

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

#24 - Plot fixes

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

#23 - Bug fixes

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

#22 - Add scaf to db

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

#21 - Intermediate genes addition

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

#20 - Clinker addition

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

#19 - do not generate linkage matrix when single result

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

#18 - Hmmer implementation & GUI updates

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

#17 - Biopython sql

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

#16 - Does the sample size(amount) affect the results of cblaster?

Issue - State: closed - Opened by jeep3 over 3 years ago

#15 - Add GenBank/EMBL parsers

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

#14 - Tb docs 241120

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

#13 - Genbank addition

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

#12 - GUI search Error

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

#11 - GUI Crashes

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

#10 - UnboundLocalError: local variable 'header' referenced before assignment

Issue - State: closed - Opened by ghost over 3 years ago - 7 comments

#9 - Additions of docstrings and removal of small errors

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