chapmanb bcbb issues - Githubissues

chapmanb / bcbb

Incubator for useful bioinformatics code, primarily in Python and R

http://bcbio.wordpress.com

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issues

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GFF.parse modifies input order of base_dict

#144 percyfal opened 3 months ago
0
Warning in GFFParser: BiopythonDeprecationWarning: UnknownSeq(length) is deprecated; please use Seq(None, length) instead.

#143 victorlin opened 5 months ago
0
Error in GFFParser: AttributeError: module 'Bio.SeqFeature' has no attribute 'SimpleLocation'

#142 victorlin opened 5 months ago
0
updates for biopython 1.82

#141 fubar2 closed 5 months ago
2
Importing BCBio.GFF suppresses Biopython warnings in external code

#140 victorlin closed 5 months ago
4
Address Biopython deprecations

#139 victorlin closed 5 months ago
6
Error in GFFParser: TypeError: SeqFeature.__init__() got an unexpected keyword argument 'strand'

#138 victorlin closed 5 months ago
1
Fix error with biopython 1.81

#137 abretaud closed 1 year ago
3
Error in GFFParser: UnknownSeq is deprecated in biopython 1.81

#136 Kmassau opened 1 year ago
7
docs: Fix a few typos

#135 timgates42 closed 5 months ago
1
Bug in v.0.6.8 in `GFF.parse`: `AttributeError: 'NoneType' object has no attribute 'find'`

#134 corneliusroemer closed 2 years ago
1
Support zero length reads in FakeHandle

#133 peterjc closed 3 years ago
1
glimmergff_to_proteins.py / Alternative Codon Table

#132 zeynepkurtw opened 3 years ago
0
glimmergff_to_proteins.py / Reordering Fasta file

#131 zeynepkurtw opened 3 years ago
0
Any chance a new release will be made sometime soon?

#130 DavyCats closed 4 months ago
0
Add license to setup.py

#129 sergiuser1 closed 4 years ago
1
IndexError with NCBI gff

#128 MrTomRod opened 4 years ago
0
py3: raise TypeError on binary file handle

#127 tipabu closed 5 years ago
1
fix crashes when parsing gtf files which contain gene lines

#126 DavyCats closed 5 years ago
0
Python 3 compatibility issue + fix

#125 DSLituiev closed 5 years ago
3
Add biopython dependency to bcbio gff

#124 rhpvorderman closed 5 years ago
1
issue with reduce

#123 zlye closed 5 years ago
5
Add LICENSE file to bcbio-gff Manifest.in

#122 dfornika closed 5 years ago
1
Need Nucleotide or protein alphabet

#121 camilo-monge closed 5 years ago
2
TypeError: 'FakeHandle' object is not iterable

#120 Rhinogradentia closed 5 years ago
2
licence?

#119 fbremer closed 5 years ago
1
Did not find remapped ID location:

#118 fbeghini opened 6 years ago
2
Mention parallel sessions; link to part 2

#117 nlharris closed 6 years ago
1
Update bosc2018_day1a.md

#116 jdidion closed 6 years ago
1
ValueError: need more than 0 values to unpack

#115 zhengboying opened 6 years ago
1
make gff_to_genbank.py with python3 compatibility

#114 hsiaoyi0504 closed 6 years ago
1
Fixed a typo

#113 hsiaoyi0504 closed 6 years ago
1
Update chapman_research_statement.org

#112 sjhosui closed 6 years ago
0
Regarding gff2_to_gff3.py script

#111 jeffinrockey opened 7 years ago
0
GFF parsing fails with most recent version of BioPython

#110 khughitt closed 7 years ago
8
GFF3 parent / id remapping issue.

#109 hexylena opened 8 years ago
2
Missing features in GFF3 data

#108 thobalose opened 8 years ago
0
sort -V option is not supported on OSX

#107 brainstorm closed 8 years ago
1
Explicitly added LICENSE file to bcbio-gff.

#106 cmclean closed 8 years ago
1
Declare dependency on biopython

#105 detrout opened 8 years ago
0
Added inferred strand for inferred parent when safe

#104 mspinelli closed 8 years ago
1
make python 3 compatible

#103 hredestig closed 8 years ago
1
write Dbxref instead of db_xref when converting genbank to GFF3

#102 timflutre opened 8 years ago
4
Convert GFF file to Sequin TBL file

#101 sjackman closed 5 years ago
11
globalenv versus globalEnv in count_diffexp (rpy2 call)

#100 yarden closed 8 years ago
2
GFF module can write unreadable GFF3 sequences.

#99 hexylena opened 9 years ago
1
Support seqid column and fix #97

#98 hexylena closed 9 years ago
1
Missing column 1 in gff3 data

#97 hexylena closed 9 years ago
2
Python 2/3 compatibiliy fixes

#96 mspinelli closed 9 years ago
1
CDS entries in GFF3 file are not merged to a CompoundLocation

#95 mikdur opened 9 years ago
5