mdmparis/defense-finder issues and pull requests

#69 - Update README.md

Pull Request - State: closed - Opened by bneron 27 days ago

#68 - [BUG] miscalculation of alignment coverage

Issue - State: open - Opened by jpjarnoux 3 months ago - 6 comments
Labels: bug

#67 - [BUG]Issue with -A Option in DefenseFinder v3.1.0

Issue - State: closed - Opened by maocheng2020 3 months ago - 2 comments
Labels: bug, stale

#66 - [BUG] Hmmer error

Issue - State: open - Opened by mesti90 3 months ago - 2 comments
Labels: bug

#65 - [HELP] How do I know how many systems and subsystems are in the current DF?

Issue - State: closed - Opened by lianmsu 4 months ago - 1 comment
Labels: help wanted, stale

#64 - Add ADF and pandas posttreatment

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

#63 - OSError: [Errno 39] Directory not empty: 'Cas'[BUG]

Issue - State: closed - Opened by chengzhongyi8 6 months ago - 1 comment
Labels: bug, stale

#62 - Fix command for creating Conda environment

Pull Request - State: closed - Opened by memgonzales 7 months ago

#61 - `replicon` fused to `sys_id` in `defense_finder_genes` output

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

#60 - No way to change macsyfinder to linear topology from circular.

Issue - State: closed - Opened by chrisdoering8197 7 months ago - 1 comment
Labels: bug, enhancement, stale

#59 - Use pandas in the post treatment

Pull Request - State: closed - Opened by FlorianTesson 8 months ago - 5 comments

#58 - Allow to specify a path to an index dir for msf

Pull Request - State: closed - Opened by jeanrjc 8 months ago - 1 comment

#57 - macsyfinder:"No such model definition: 'defense-finder-models'"

Issue - State: closed - Opened by yaojian1997 8 months ago - 1 comment

#56 - No such profile error in version 1.2.2

Issue - State: closed - Opened by roo-weed 8 months ago - 1 comment

#55 - What's the SOFIC system, we cannot find the reference article about this.

Issue - State: closed - Opened by liaohu1231 9 months ago - 2 comments

#54 - sort lines before comparing them to improve test readability

Pull Request - State: closed - Opened by bryan-brancotte 10 months ago - 1 comment

#53 - Test more python versions

Pull Request - State: closed - Opened by bryan-brancotte 10 months ago - 1 comment

#52 - Alignment availability for RefSeq

Issue - State: closed - Opened by Ge0rges 10 months ago - 2 comments

#51 - Column header definitions and criteria for an HMM hit being listed in Systems or Genes tsv files

Issue - State: closed - Opened by asantia3 10 months ago - 1 comment
Labels: stale

#50 - use latest source from macsyfinder

Pull Request - State: closed - Opened by bryan-brancotte 10 months ago - 1 comment

#49 - Question of reduce the iops of shared-disk operations

Issue - State: closed - Opened by cron-weasley 10 months ago - 1 comment
Labels: stale

#48 - Duplicated sequences while using pyrodigal when multiple FNA

Issue - State: closed - Opened by FlorianTesson 10 months ago
Labels: bug

#47 - use tagged version not latest from sources

Pull Request - State: closed - Opened by bryan-brancotte 10 months ago - 1 comment
Labels: stale-PR

#46 - error when using unordered db-type

Issue - State: closed - Opened by schmittel 10 months ago - 4 comments

#45 - How to use Defensefinder for each draft genome or each MAG?

Issue - State: closed - Opened by actledge 11 months ago - 2 comments
Labels: stale

#44 - AttributeError: 'NoneType' object has no attribute 'split'

Issue - State: closed - Opened by liucong2016 11 months ago - 3 comments
Labels: no-issue-activity, stale

#43 - Errno 39: Directory not empty: 'Cas'

Issue - State: closed - Opened by amorrod 11 months ago - 2 comments
Labels: no-issue-activity, stale

#42 - macsypy.error.MacsypyError: 'defense-finder-models/Rst_Hydrolase-Tm__Hydrolase-Tm': No such profile

Issue - State: closed - Opened by ezherman 11 months ago - 6 comments

#41 - allow to force reinstall models

Pull Request - State: closed - Opened by bryan-brancotte 11 months ago - 2 comments

#40 - --db-type unordered is not processed correctly

Issue - State: closed - Opened by jeanrjc 12 months ago - 6 comments
Labels: bug, stale

#39 - Defense finder failed to run

Issue - State: closed - Opened by sujeetpowar 12 months ago - 1 comment

#38 - Inconsistencies between versions and local VS webserver results.

Issue - State: closed - Opened by TaraBartolec 12 months ago - 3 comments
Labels: no-issue-activity, stale

#37 - Issue with defense_finder_posttreat for "aa" protein files

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

#36 - macsyfinder: "No such model definition: 'CasFinder'"

Issue - State: closed - Opened by liaohu1231 about 1 year ago - 10 comments
Labels: no-issue-activity, stale

#35 - Draft: Add functional test

Pull Request - State: closed - Opened by bryan-brancotte about 1 year ago - 5 comments

#34 - Command to update models

Issue - State: closed - Opened by rplanel about 1 year ago - 2 comments
Labels: bug, no-issue-activity

#33 - add possibility to run defensefinder on a nucleotide fasta

Pull Request - State: closed - Opened by jeanrjc about 1 year ago - 1 comment

#32 - hmmsearch not honouring -w --workers

Issue - State: closed - Opened by tsp-kucbd about 1 year ago - 1 comment

#31 - Feature msfv2 support

Pull Request - State: closed - Opened by bneron about 1 year ago

#30 - an error occurred during Hmmer execution: command = hmmsearch

Issue - State: closed - Opened by davidmadariaga about 1 year ago - 1 comment

#29 - AttributeError: 'DataFrame' object has no attribute 'append'. Did you mean: '_append'?

Issue - State: closed - Opened by joelwwh over 1 year ago - 3 comments
Labels: no-issue-activity, stale

#28 - webserver

Issue - State: closed - Opened by drp223 over 1 year ago - 1 comment

#27 - Where are all bit score cutoffs reported? Missing for some systems in Liste_hmm_system.md

Issue - State: closed - Opened by scubalaina over 1 year ago - 2 comments
Labels: no-issue-activity, stale

#26 - Something wrong when I run until “Computing best solutions for UserReplicon ”

Issue - State: closed - Opened by gjzheng over 1 year ago - 3 comments
Labels: stale

#25 - request: add defense-finder to bioconda

Issue - State: closed - Opened by alexweisberg over 1 year ago - 2 comments

#24 - defense-finder update error

Issue - State: closed - Opened by nayeon1994 almost 2 years ago - 1 comment
Labels: stale

#23 - defense-finder update error: IndexError: list index out of range | issue downloading models

Issue - State: closed - Opened by scubalaina almost 2 years ago - 5 comments
Labels: stale

#22 - Difference between number of HMM and Liste of hmm file

Issue - State: closed - Opened by jpjarnoux almost 2 years ago - 1 comment
Labels: stale

#21 - IndexError: list index out of range when running 'defense-finder update'

Issue - State: closed - Opened by ZongzhiWu almost 2 years ago - 2 comments
Labels: stale

#20 - Macsyfinder best_solution.tsv parsing error and suggested solution

Issue - State: closed - Opened by hsbi almost 2 years ago - 3 comments
Labels: stale

#19 - FileNotFoundError: [Errno 2] No such file or directory: '/defense-finder-tmp/RM/best_solution.tsv' when using --db-type unordered

Issue - State: closed - Opened by felipehcoutinho about 2 years ago - 3 comments
Labels: stale

GitHub / mdmparis/defense-finder issues and pull requests