chapmanb/bcbb issues and pull requests

#146 - distribute_setup.py: migrate away from distutils.

Pull Request - State: open - Opened by emollier 3 months ago

#145 - GFFParser.py: fix SyntaxWarning.

Pull Request - State: open - Opened by emollier 3 months ago

#144 - GFF.parse modifies input order of base_dict

Issue - State: open - Opened by percyfal 11 months ago

#143 - Warning in GFFParser: BiopythonDeprecationWarning: UnknownSeq(length) is deprecated; please use Seq(None, length) instead.

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

#142 - Error in GFFParser: AttributeError: module 'Bio.SeqFeature' has no attribute 'SimpleLocation'

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

#141 - updates for biopython 1.82

Pull Request - State: closed - Opened by fubar2 about 1 year ago - 2 comments

#140 - Importing BCBio.GFF suppresses Biopython warnings in external code

Issue - State: closed - Opened by victorlin about 1 year ago - 4 comments

#139 - Address Biopython deprecations

Pull Request - State: closed - Opened by victorlin about 1 year ago - 6 comments

#138 - Error in GFFParser: TypeError: SeqFeature.init() got an unexpected keyword argument 'strand'

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

#137 - Fix error with biopython 1.81

Pull Request - State: closed - Opened by abretaud almost 2 years ago - 3 comments

#136 - Error in GFFParser: UnknownSeq is deprecated in biopython 1.81

Issue - State: open - Opened by Kmassau almost 2 years ago - 7 comments

#135 - docs: Fix a few typos

Pull Request - State: closed - Opened by timgates42 over 2 years ago - 1 comment

#134 - Bug in v.0.6.8 in `GFF.parse`: `AttributeError: 'NoneType' object has no attribute 'find'`

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

#133 - Support zero length reads in FakeHandle

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

#132 - glimmergff_to_proteins.py / Alternative Codon Table

Issue - State: open - Opened by zeynepkurtw over 4 years ago

#131 - glimmergff_to_proteins.py / Reordering Fasta file

Issue - State: open - Opened by zeynepkurtw over 4 years ago

#130 - Any chance a new release will be made sometime soon?

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

#129 - Add license to setup.py

Pull Request - State: closed - Opened by sergiuser1 almost 5 years ago - 1 comment

#128 - IndexError with NCBI gff

Issue - State: open - Opened by MrTomRod about 5 years ago

#127 - py3: raise TypeError on binary file handle

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

#126 - fix crashes when parsing gtf files which contain gene lines

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

#125 - Python 3 compatibility issue + fix

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

#124 - Add biopython dependency to bcbio gff

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

#123 - issue with reduce

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

#122 - Add LICENSE file to bcbio-gff Manifest.in

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

#121 - Need Nucleotide or protein alphabet

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

#120 - TypeError: 'FakeHandle' object is not iterable

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

#119 - licence?

Issue - State: closed - Opened by fbremer over 6 years ago - 1 comment

#118 - Did not find remapped ID location:

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

#117 - Mention parallel sessions; link to part 2

Pull Request - State: closed - Opened by nlharris over 6 years ago - 1 comment

#116 - Update bosc2018_day1a.md

Pull Request - State: closed - Opened by jdidion over 6 years ago - 1 comment

#115 - ValueError: need more than 0 values to unpack

Issue - State: open - Opened by zhengboying almost 7 years ago - 1 comment

#114 - make gff_to_genbank.py with python3 compatibility

Pull Request - State: closed - Opened by hsiaoyi0504 almost 7 years ago - 1 comment

#113 - Fixed a typo

Pull Request - State: closed - Opened by hsiaoyi0504 almost 7 years ago - 1 comment

#112 - Update chapman_research_statement.org

Pull Request - State: closed - Opened by sjhosui over 7 years ago

#111 - Regarding gff2_to_gff3.py script

Issue - State: open - Opened by jeffinrockey over 8 years ago

#110 - GFF parsing fails with most recent version of BioPython

Issue - State: closed - Opened by khughitt over 8 years ago - 8 comments

#109 - GFF3 parent / id remapping issue.

Issue - State: open - Opened by hexylena over 8 years ago - 2 comments

#108 - Missing features in GFF3 data

Issue - State: open - Opened by thobalose almost 9 years ago

#107 - sort -V option is not supported on OSX

Pull Request - State: closed - Opened by brainstorm about 9 years ago - 1 comment

#106 - Explicitly added LICENSE file to bcbio-gff.

Pull Request - State: closed - Opened by cmclean about 9 years ago - 1 comment

#105 - Declare dependency on biopython

Issue - State: open - Opened by detrout about 9 years ago

#104 - Added inferred strand for inferred parent when safe

Pull Request - State: closed - Opened by mspinelli about 9 years ago - 1 comment

#103 - make python 3 compatible

Pull Request - State: closed - Opened by hredestig over 9 years ago - 1 comment

#102 - write Dbxref instead of db_xref when converting genbank to GFF3

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

#101 - Convert GFF file to Sequin TBL file

Issue - State: closed - Opened by sjackman over 9 years ago - 11 comments

#100 - globalenv versus globalEnv in count_diffexp (rpy2 call)

Issue - State: closed - Opened by yarden over 9 years ago - 2 comments

#99 - GFF module can write unreadable GFF3 sequences.

Issue - State: open - Opened by hexylena over 9 years ago - 1 comment

#98 - Support seqid column and fix #97

Pull Request - State: closed - Opened by hexylena almost 10 years ago - 1 comment

#97 - Missing column 1 in gff3 data

Issue - State: closed - Opened by hexylena almost 10 years ago - 2 comments

#96 - Python 2/3 compatibiliy fixes

Pull Request - State: closed - Opened by mspinelli about 10 years ago - 1 comment

#95 - CDS entries in GFF3 file are not merged to a CompoundLocation

Issue - State: open - Opened by mikdur about 10 years ago - 5 comments

#94 - A few things I noticed

Pull Request - State: closed - Opened by jwm about 10 years ago - 1 comment

#93 - Fix typo in mkdir command

Pull Request - State: closed - Opened by jwm about 10 years ago

#92 - tabix access to gff?

Issue - State: closed - Opened by danielecook over 10 years ago - 1 comment

#91 - Trans-spliced genes cause ValueError: Did not find remapped ID location

Issue - State: closed - Opened by sjackman over 10 years ago - 5 comments

#90 - GFFOutput.py

Pull Request - State: closed - Opened by TheOneHyer over 10 years ago - 5 comments

#89 - GFF parsing stopped working on system upgrade - biopython error

Issue - State: closed - Opened by patena over 10 years ago - 2 comments

#88 - parsing of GFF3 attributes fails when tag starts with a space

Issue - State: closed - Opened by wholtz over 10 years ago - 1 comment

#87 - CDS Phase not calculated by GFFOutput

Issue - State: closed - Opened by bobbyo almost 11 years ago - 1 comment

#86 - over url-encoding in attribute fields

Issue - State: open - Opened by bobbyo almost 11 years ago - 5 comments

#85 - parse simple returns different start location

Issue - State: closed - Opened by NtBaru almost 11 years ago - 2 comments

#84 - adaptor_trim.py

Issue - State: closed - Opened by radaniba almost 11 years ago - 2 comments

#83 - BUG report

Pull Request - State: closed - Opened by Hugh-Zhu almost 11 years ago - 2 comments

#82 - gff_to_genbank.py: sub_features is deprecated

Issue - State: closed - Opened by sjackman almost 11 years ago - 2 comments

#81 - GFF code does not work in Python 3

Issue - State: closed - Opened by tiagoantao about 11 years ago - 7 comments

#80 - GFF: parse_simple fails in some cases

Issue - State: closed - Opened by khughitt about 11 years ago - 1 comment

#79 - GFFparser only keeps first line

Issue - State: closed - Opened by khughitt about 11 years ago - 2 comments

#78 - Added Python 3 support to GFF parser

Pull Request - State: closed - Opened by khughitt about 11 years ago - 2 comments

#77 - GFF.parser target_lines returns interchange order of contigs if contigs sorted in certain order

Issue - State: closed - Opened by genestack-solomatin over 11 years ago - 1 comment

#76 - GFFParser on python 3.3.2

Issue - State: closed - Opened by ychenbioinfo over 11 years ago - 1 comment

#75 - GFF parsing with initial sequence fails

Issue - State: closed - Opened by benjiec over 11 years ago - 2 comments

#74 - import error on Mac OS X

Issue - State: closed - Opened by ghost over 11 years ago - 2 comments

#73 - Update plink_to_vcf.py

Pull Request - State: closed - Opened by kyzhao almost 12 years ago - 1 comment