bioperl/bioperl-live issues and pull requests

#393 - Could Bio::DB::Fasta support gzipped FASTA?

Issue - State: open - Opened by Tong-Chen 21 days ago

#392 - Alternative CI?

Issue - State: closed - Opened by cjfields 5 months ago - 2 comments

#391 - Bio::Tools::CodonTable is out of date (again)

Issue - State: closed - Opened by carandraug 5 months ago - 2 comments

#390 - Update CodonTable.pm with Genetic code 15

Pull Request - State: closed - Opened by igortru 5 months ago - 1 comment

#389 - Genetic code 15 need to be supported

Issue - State: closed - Opened by igortru 5 months ago - 5 comments

#388 - Bio::Tools::GFF add extra empty attribute problematic

Issue - State: open - Opened by Juke34 6 months ago - 1 comment

#387 - Bug in is_ter_codon

Pull Request - State: closed - Opened by Juke34 8 months ago - 3 comments

#386 - Codontable bugs.

Pull Request - State: closed - Opened by Juke34 8 months ago - 1 comment

#385 - t/Root/RootIO.t may fail because of Google returning 403

Issue - State: closed - Opened by eserte 8 months ago - 4 comments

#384 - cant run VAMPr because of Bio::DB::Fasta

Issue - State: closed - Opened by Hedi65 10 months ago - 1 comment

#383 - Fix tiny bug

Pull Request - State: closed - Opened by Juke34 about 1 year ago - 4 comments

#382 - fix a tiny typo

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

#381 - Fix bsml_sax.t by using lax SAX parser

Pull Request - State: closed - Opened by zmughal over 1 year ago - 3 comments

#380 - Add minimum dependency on base.pm v2.18

Pull Request - State: closed - Opened by zmughal over 1 year ago - 2 comments

#379 - CI: Add test jobs using Debian containers

Pull Request - State: closed - Opened by zmughal over 1 year ago - 2 comments

#378 - CI: test with minimum, median, and latest Perl versions

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

#377 - Suggestion: create a CODEOWNERS file to connect modules with maintainers

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

#376 - Failing t/SeqIO/bsml_sax.t due to 404 for DTD URL

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

#375 - Minimum Perl version should be set to v5.8

Issue - State: open - Opened by zmughal over 1 year ago - 6 comments

#374 - Add initial GitHub Actions workflow

Pull Request - State: closed - Opened by zmughal over 1 year ago - 16 comments

#373 - How do I grab the corresponding sequence from the mitochondrial genome?

Issue - State: closed - Opened by CC3729 over 1 year ago - 3 comments

#372 - Why Bio::SeqFeature::Generic can only get Seqfeature's source item?

Issue - State: closed - Opened by CC3729 almost 2 years ago - 3 comments

#371 - Why Bio::SeqFeature::Generic can only get Seqfeature's source item?

Issue - State: closed - Opened by CC3729 almost 2 years ago - 1 comment

#370 - fix for writing large_fasta sequences

Pull Request - State: closed - Opened by epaule over 2 years ago - 3 comments

#369 - Bio::Tools::GFF doesn't write eukaryotic multi-exon genes correctly

Issue - State: open - Opened by krobison13 over 2 years ago - 7 comments

#368 - make a CITATION.cff?

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

#367 - How to install Bioperl v1.7.2 in Ubuntu

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

#366 - Create CODE_OF_CONDUCT.md

Pull Request - State: closed - Opened by cjfields over 2 years ago - 9 comments

#365 - Add Code of Conduct for OBF

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

#364 - Taxonomy.t Tests Fails for Bio::Perl::

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

#363 - Bio::DB:Taxonomy won't connect to NCBI

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

#362 - t/SeqFeature/Generic.t failures

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

#361 - Update bp_seqcut

Pull Request - State: closed - Opened by MattOates about 3 years ago - 1 comment

#360 - problem with installing Bio::DB::Fasta module

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

#359 - Research notice: Sustainability in Open Source Projects

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

#358 - adds research notice to the readme

Pull Request - State: closed - Opened by yochannah over 3 years ago - 6 comments

#357 - Bio::Align::DNAStatistics to calculate Tajima-Nei Distance Fail

Issue - State: closed - Opened by MauriAndresMU1313 over 3 years ago - 6 comments

#356 - Testing Bio::DB::NCBIHelper-1.7.6 failed

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

#355 - Possible precedence issue with control flow operator at Bio/DB/IndexedBase.pm line 805

Issue - State: open - Opened by hyphaltip over 3 years ago - 3 comments
Labels: Blocker

#354 - Bio::Procedural won't install

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

#353 - Unable to run ping_ensembl.pl

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

#352 - Bio/SeqIO.pm

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

#351 - Where to find moved packages?

Issue - State: closed - Opened by Stikus almost 4 years ago - 5 comments

#350 - db.h dependency

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

#349 - Sequin table format

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

#348 - Adjust Swiss-Prot FT A..B lines

Pull Request - State: closed - Opened by smoe almost 4 years ago - 1 comment

#347 - Remove XML::DOM::XPath dependency

Issue - State: closed - Opened by cjfields almost 4 years ago - 10 comments
Labels: Code split, Blocker

#346 - Updating Mauricio's email

Pull Request - State: closed - Opened by arareko about 4 years ago

#345 - Each line of the file must be less than 65,536 characters

Issue - State: open - Opened by Juke34 over 4 years ago - 9 comments

#344 - Installation of Bio::Tree::Tree fails under perl-5.30.3

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

#343 - examples: remove note about contacting the author

Pull Request - State: closed - Opened by kortschak over 4 years ago - 1 comment

#342 - Can't locate object method "no_sequences" via package "Bio::SimpleAlign"

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

#341 - Error thrown in OBO file parsing

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

#340 - EXCEPTION: Bio::Root::Exception Inappropriate ioctl for device

Issue - State: open - Opened by moldach over 4 years ago - 5 comments

#339 - Update %FTQUAL_NO_QUOTE: List of qualifiers without quote.

Pull Request - State: closed - Opened by hdevillers over 4 years ago - 1 comment

#338 - Build failure until I used cpanm --force, on Mac OS X Catalina

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

#337 - Problem with test for Bio::Root::HTTPget

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

#336 - Problem installing cpan Bio::Tree::Tree

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

#334 - bioperl install fails due to failure in XML::DOM::XPath

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

#333 - Problem with Bio::AlignIO::meme

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

#332 - Why version 1.7.7 is not a release?

Issue - State: closed - Opened by serge2016 over 4 years ago - 1 comment

#331 - Circular dependency

Issue - State: closed - Opened by euduca almost 5 years ago - 6 comments

#330 - homepage in dist.ini 404s

Issue - State: closed - Opened by mr-c almost 5 years ago - 4 comments

#329 - t/Tree/TreeStatistics.t failures

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

#328 - Debian "lintian" inspired spelling fixes

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

#327 - Bio::Tools::GFF _gffX_string update

Issue - State: open - Opened by Juke34 almost 5 years ago - 1 comment

#326 - Fails if GD.pm is not installed

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

#325 - Travis-CI test issues

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

#324 - Bio::Assembly still listed in HACKING.md

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

#323 - t/00-compile.t fails without GD.pm

Issue - State: closed - Opened by eserte about 5 years ago - 6 comments

#321 - Bioperl outputs invalid Genbank/EMBL

Issue - State: closed - Opened by innovate-invent over 5 years ago - 6 comments

#320 - SVG coveralls badge

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

#319 - Reduce the number of indirect object calls

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

#318 - MapTiling Root Exception error

Issue - State: closed - Opened by ghanashyamchalla over 5 years ago - 7 comments

#317 - transfer-bootstrap-expectation

Pull Request - State: closed - Opened by lskatz over 5 years ago - 3 comments

#316 - Can't get the specific sequence via seq id

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

#315 - Fix Codon Table 0 (strict) that was not selectable

Pull Request - State: closed - Opened by Juke34 over 5 years ago - 1 comment

#314 - onerous installation

Issue - State: open - Opened by tjparnell over 5 years ago - 12 comments

#313 - LWP::Protocol::https required in test suite

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

#312 - Enable TblastN parsing

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

#311 - Minus and Plus HSP misattributed

Issue - State: open - Opened by FredericBGA over 5 years ago - 1 comment

#310 - Move maint email address to something I'll see

Pull Request - State: closed - Opened by MattOates over 5 years ago - 1 comment

#309 - replacing all calls to Bio::DB::IndexedBase::_strip_crnl with native perl tr operator

Pull Request - State: closed - Opened by carsonhh over 5 years ago - 1 comment

#308 - bp_classify_hits_kingdom needs HOME on env

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

#307 - Can't locate object method "new" via package "Bio::Search::HSP::GenericHSP::SUPER"

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

#306 - Wrong metadata (repository, issues)

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

#305 - Simplify Bio::DB::IndexedBase?

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

#304 - fixed bootstrapping bug where no bootstrap could have been 100 percent

Pull Request - State: closed - Opened by lskatz over 5 years ago - 1 comment

#303 - Bio::DB::IndexedBase unable to open index file

Issue - State: closed - Opened by walkeryp almost 6 years ago - 2 comments

#301 - ‎The DDBJ/ENA/GenBank accession number change

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

#299 - WebDBSeqI Request Error

Issue - State: closed - Opened by WangJian99 almost 6 years ago - 2 comments

#298 - Change Nexus syntax in output from Bio::AlignIO::nexus

Issue - State: open - Opened by nylander almost 6 years ago - 1 comment

#297 - Bio::SeqIO cannot locate Bio::SeqIO::fasta

Issue - State: closed - Opened by ChenXingguo almost 6 years ago - 2 comments

#296 - failing test for SeqTools/SeqUtils.t

Issue - State: closed - Opened by hlapp about 6 years ago - 2 comments

#295 - failing test for SeqFeature/Generic.t

Issue - State: closed - Opened by hlapp about 6 years ago - 1 comment

#294 - deprecating Bio::Root::RootI::deprecate

Issue - State: closed - Opened by carandraug about 6 years ago - 4 comments

#293 - failing tests for Bio::DB::SwissProt

Issue - State: closed - Opened by carandraug about 6 years ago - 3 comments
Labels: RemoteDB

GitHub / bioperl/bioperl-live issues and pull requests