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chapmanb
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bcbb
Incubator for useful bioinformatics code, primarily in Python and R
http://bcbio.wordpress.com
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GFF.parse modifies input order of base_dict
#144
percyfal
opened
6 months ago
0
Warning in GFFParser: BiopythonDeprecationWarning: UnknownSeq(length) is deprecated; please use Seq(None, length) instead.
#143
victorlin
opened
8 months ago
0
Error in GFFParser: AttributeError: module 'Bio.SeqFeature' has no attribute 'SimpleLocation'
#142
victorlin
opened
8 months ago
0
updates for biopython 1.82
#141
fubar2
closed
8 months ago
2
Importing BCBio.GFF suppresses Biopython warnings in external code
#140
victorlin
closed
8 months ago
4
Address Biopython deprecations
#139
victorlin
closed
8 months ago
6
Error in GFFParser: TypeError: SeqFeature.__init__() got an unexpected keyword argument 'strand'
#138
victorlin
closed
8 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
8 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
zeyak
opened
4 years ago
0
glimmergff_to_proteins.py / Reordering Fasta file
#131
zeyak
opened
4 years ago
0
Any chance a new release will be made sometime soon?
#130
DavyCats
closed
7 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
6 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
7 years ago
0
Regarding gff2_to_gff3.py script
#111
jeffinrockey
opened
8 years ago
0
GFF parsing fails with most recent version of BioPython
#110
khughitt
closed
8 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
6 years ago
11
globalenv versus globalEnv in count_diffexp (rpy2 call)
#100
yarden
closed
9 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
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