gem-pasteur/Integron_Finder issues and pull requests

#113 - [FEAT] Use the option --prot-file independently of the option --annot-parser

Issue - State: open - Opened by LCoffion 7 months ago
Labels: enhancement

#112 - [FEAT] improve IF to work with gembase 2

Issue - State: open - Opened by bneron 9 months ago
Labels: enhancement

#111 - [FEAT] Remove/Relax Matplotlib version requirement

Issue - State: open - Opened by acarafat 9 months ago - 5 comments
Labels: enhancement

#110 - [HELP] In silico IntI1 qPCR assay don't match results IntegronFinder

Issue - State: closed - Opened by LauraVP1994 10 months ago - 10 comments
Labels: help wanted

#109 - [HELP] Different results in hits between multi-gbk and merged gbk on same sample?

Issue - State: closed - Opened by Svnipni 11 months ago - 2 comments
Labels: help wanted

#108 - AttributeError: module 'Bio.Seq' has no attribute 'IUPAC'

Issue - State: closed - Opened by EllBaum about 1 year ago - 2 comments
Labels: help wanted

#107 - [BUG] underlay of /etc/localtime required more than 50 (87) bind mounts

Issue - State: closed - Opened by yegonzalezflores over 1 year ago - 4 comments
Labels: bug

#106 - How to use --func-annot

Issue - State: closed - Opened by aslangabriel over 1 year ago - 1 comment
Labels: help wanted

#105 - [HELP] How can I get the sequence of whole integron?

Issue - State: closed - Opened by Galib009 over 1 year ago - 3 comments
Labels: help wanted

#104 - [BUG] IF crashes with --gbk option in a specific caase

Issue - State: open - Opened by eloilit over 1 year ago - 3 comments
Labels: bug

#103 - [BUG] IF crashes on a multiple contigs file

Issue - State: closed - Opened by eloilit almost 2 years ago - 1 comment
Labels: bug

#102 - [HELP] Question: are gene cassettes of a integron all on the same strand?

Issue - State: closed - Opened by jiarong almost 2 years ago - 4 comments
Labels: help wanted

#101 - [HELP] Question: are the integrase (IntI) always on the opposite strand of gene cassettes?

Issue - State: closed - Opened by jiarong almost 2 years ago - 3 comments
Labels: help wanted

#100 - [FEAT] genbank or gff as input

Issue - State: open - Opened by alexweisberg almost 2 years ago
Labels: enhancement

#99 - [BUG] IntegronFinder fails when there is a "space" in the path

Issue - State: closed - Opened by eloilit almost 2 years ago - 1 comment
Labels: bug

#98 - :pencil2: Eloilit patch issue 97 on CPU documentation

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

#97 - [FEAT] Add documentation about CPU usage

Issue - State: closed - Opened by eloilit almost 2 years ago
Labels: enhancement

#96 - install Integron_Finder through conda

Issue - State: closed - Opened by danielarothschild over 2 years ago

#95 - Complete documentation for ARG

Issue - State: closed - Opened by jeanrjc over 2 years ago - 1 comment
Labels: enhancement, doc

#94 - IntegronFinder does not pass unitary test "test_main_outdir_exists" (test_merge.TestMain)

Issue - State: closed - Opened by eloilit over 2 years ago

#93 - Issue with colorlog logging

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

#92 - ValueError: attempt to get argmin of an empty sequence

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

#91 - IF give different results depending installation

Issue - State: closed - Opened by bneron almost 3 years ago - 2 comments
Labels: bug, high priority

#90 - Integron_Finder bogs down server's I/O when ran on metagenomes with ~million contigs

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

#89 - update hmmsearch command line and profile

Issue - State: closed - Opened by bneron almost 3 years ago
Labels: enhancement

#88 - IntegronFinder should not run twice over the the edge of the replicon

Issue - State: closed - Opened by jeanrjc about 3 years ago
Labels: bug

#87 - Help me understanding the output of IF with a multi-fasta file

Issue - State: closed - Opened by bramvandijk88 about 3 years ago - 2 comments

#86 - Fatal error: Exit code 127 ()

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

#85 - End location (191284) must be greater than or equal to start location (271412)

Issue - State: closed - Opened by erichy91 about 3 years ago - 6 comments
Labels: bug, high priority

#84 - Keep attC sites even if the evalue change with local_max

Issue - State: closed - Opened by jeanrjc about 3 years ago
Labels: bug

#83 - program not work for Staphylococcus aureus

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

#82 - Problem installing integron_finder via bioconda

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

#81 - some major and common problems

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

#80 - error on calling --gembases option

Issue - State: closed - Opened by cachapuz2001 over 3 years ago - 1 comment

#79 - Error related to prodigal: RuntimeError("{0} failed returncode = {1}".format(prodigal_cmd, returncode))

Issue - State: closed - Opened by sasonbol over 3 years ago - 16 comments

#78 - AttributeError: module 'Bio.Seq' has no attribute 'IUPAC'

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

#77 - conda install causes pandas.io.common ImportError

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

#76 - Error running Singularity

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

#75 - Integron classes 1,2,3

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

#74 - Installing from pip not working

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

#73 - go_left = (full_element[full_element.type_elt == "attC"].pos_beg.values[0] - df_max.pos_end.values[0]: index 0 is out of bounds for axis 0 with size 0

Issue - State: closed - Opened by vbrover over 4 years ago - 6 comments
Labels: bug, high priority

#72 - "integron_finder --local_max --func_annot mysequences.fst" should be "integron_finder --local-max --func-annot mysequences.fst"

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

#71 - IndexError attc.py

Issue - State: closed - Opened by jfourquet2 over 4 years ago - 4 comments

#70 - Topology issues

Issue - State: closed - Opened by jeanrjc over 4 years ago - 2 comments
Labels: bug, high priority, easyfix

#69 - problem with overlapping/near identical attC sites

Issue - State: closed - Opened by jeanrjc over 4 years ago - 6 comments
Labels: bug, easyfix

#68 - in summary output, add the size of contig

Issue - State: closed - Opened by jeanrjc over 4 years ago
Labels: enhancement, easyfix

#67 - ID_integron should not be in .summary file

Issue - State: closed - Opened by jeanrjc over 4 years ago - 1 comment
Labels: bug, easyfix

#66 - summary files should be created when no integron is found

Issue - State: closed - Opened by jeanrjc over 4 years ago - 2 comments
Labels: enhancement, easyfix

#65 - bug in .integrons output

Issue - State: closed - Opened by jeanrjc over 4 years ago
Labels: bug, easyfix

#64 - Cannot install

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

#63 - Trouble installing integron_finder using pip install

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

#62 - errors

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

#61 - I cannot find intergron_Finder in bioconda

Issue - State: closed - Opened by glichtenstein about 5 years ago - 4 comments

#60 - preparation problems

Issue - State: closed - Opened by aslangabriel over 5 years ago - 11 comments

#59 - Added newlines

Pull Request - State: closed - Opened by g1o over 5 years ago - 2 comments

#58 - Runtime error on draft assemblies

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

#57 - installing Integron_Finderv2 on conda

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

#56 - Invalid characters

Issue - State: closed - Opened by pbravakos over 5 years ago - 4 comments

#55 - Prediction over sequence start with --linear

Issue - State: closed - Opened by johrollin almost 6 years ago - 4 comments
Labels: bug

#54 - add github page for khillion

Pull Request - State: closed - Opened by khillion almost 6 years ago - 1 comment

#53 - Small change to keep it up with the matplot version

Pull Request - State: closed - Opened by g1o about 6 years ago - 1 comment

#52 - -vv does not work

Issue - State: closed - Opened by bneron over 6 years ago
Labels: bug, high priority

#51 - Small change to check pipeline

Pull Request - State: closed - Opened by aperrin over 6 years ago

#50 - Complete Documentation with all new options and changes

Issue - State: closed - Opened by jeanrjc over 6 years ago
Labels: doc, high priority

#49 - log file

Issue - State: closed - Opened by asetGem over 6 years ago
Labels: enhancement, high priority

#48 - Add function parsing attC sites

Issue - State: closed - Opened by asetGem over 6 years ago - 1 comment
Labels: enhancement, low priority

#47 - stdout/stderr management

Issue - State: closed - Opened by asetGem over 6 years ago - 3 comments
Labels: enhancement, medium priority

#46 - Diversify installation

Issue - State: closed - Opened by asetGem over 6 years ago
Labels: installation, medium priority

#45 - Add threshold of number of attC to keep a CALIN

Issue - State: closed - Opened by asetGem over 6 years ago - 1 comment
Labels: enhancement, low priority

#44 - Parallelisation

Issue - State: closed - Opened by asetGem over 6 years ago - 1 comment
Labels: enhancement, medium priority

#43 - Circularity with multi-fasta input

Issue - State: closed - Opened by asetGem over 6 years ago - 3 comments
Labels: enhancement, high priority

#42 - Improve error handling

Issue - State: closed - Opened by asetGem over 6 years ago - 4 comments
Labels: enhancement, medium priority

#41 - Handle multi-fasta input files

Issue - State: closed - Opened by asetGem over 6 years ago - 1 comment
Labels: enhancement, high priority

#40 - Modify default outputs

Issue - State: closed - Opened by asetGem over 6 years ago - 1 comment
Labels: enhancement, high priority

#39 - Add information on running tests in doc

Issue - State: closed - Opened by asetGem over 6 years ago - 1 comment
Labels: doc, high priority

#38 - add unit test for all Integron methods

Issue - State: closed - Opened by bneron about 7 years ago
Labels: testing

#37 - remove accent for XML compatibility

Pull Request - State: closed - Opened by khillion about 7 years ago

#36 - Find integrons in a multiple sequence fasta file

Issue - State: closed - Opened by koopkaup about 7 years ago - 2 comments

#35 - help --gembase

Issue - State: closed - Opened by johrollin about 7 years ago - 5 comments