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mdshw5
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pyfaidx
Efficient pythonic random access to fasta subsequences
https://pypi.python.org/pypi/pyfaidx
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Fix TypeError with faidx --transform nucleotide
#172
jvierstra
closed
3 years ago
1
How to specify how the consensus sequence should be built?
#171
larahurban
closed
3 years ago
2
Make line endings survive round-trip
#170
mdshw5
opened
3 years ago
0
Load an existing .fai?
#169
rickbeeloo
closed
3 years ago
1
Implement fsspec in place of open
#168
hardingnj
closed
2 years ago
13
Device or resource busy
#167
nick-youngblut
closed
4 years ago
4
Fix write_fai
#166
folded
closed
4 years ago
1
usage on google cloud storage and more general file handling
#165
hardingnj
closed
2 years ago
1
Support for constructing and using GZI format files for BGZF compressed FASTA
#164
mdshw5
opened
4 years ago
2
Minor improvement in integer indexing Fasta class.
#163
C-nit
closed
4 years ago
2
question for Iterator mode
#162
yhgon
closed
4 years ago
2
Enable pyfaidx to accept gcp paths for compressed fasta files
#161
archanaraja
opened
4 years ago
2
Index failes if more than one empty line
#160
openpaul
opened
4 years ago
3
Unhandled exception when opening header only file
#159
openpaul
closed
4 years ago
6
implement Sequence.__eq__
#158
Maarten-vd-Sande
closed
4 years ago
4
Fasta instances should have a __len__ method
#157
mdshw5
closed
4 years ago
0
Fasta more dict-like behaviour
#156
Maarten-vd-Sande
closed
4 years ago
12
Support zero-length sequences
#155
prihoda
closed
4 years ago
3
--split-files
#154
nservant
closed
2 years ago
2
BGZip slow performance near end of chromosomes
#153
davmlaw
opened
5 years ago
3
Cannot use FastaVariant without genotype
#152
victorlin
closed
5 years ago
2
FIX bgzip link
#151
VarIr
closed
5 years ago
1
False duplicate key error
#150
Benjamin-Lee
closed
5 years ago
1
Make pyfaidx available on py3.7
#149
VidJa
closed
5 years ago
2
fix misformatted line in README
#148
hsiaoyi0504
closed
5 years ago
1
ImportError: BioPython >= 1.73 must be installed to read block gzip files.
#147
fungs
closed
5 years ago
6
UnicodeDecodeError while reading file: how to explicit decode format?
#146
LucaCappelletti94
closed
5 years ago
3
Python 3.7: RuntimeError: generator raised StopIteration
#145
tillea
closed
5 years ago
3
Parser breaks if FASTA file does not contain >
#144
Benjamin-Lee
closed
5 years ago
6
Add support for reading from S3
#143
palakpsheth
closed
5 years ago
0
allow -v to be specified alongside -g
#142
daler
closed
6 years ago
3
Carriage return breaks parsing
#141
Benjamin-Lee
closed
6 years ago
8
The default_seq argument is not supported with using BGZF compression.
#140
UnkindPartition
closed
6 years ago
4
Obtain numpy array for sequence
#139
alimanfoo
closed
6 years ago
8
Pass build_index to Fasta constructor
#138
marcelm
closed
6 years ago
5
Large faidx. Huge memory usage?
#137
aswarren
closed
6 years ago
4
Rewrite documentation
#136
mdshw5
opened
6 years ago
0
Pull changes from issue #134
#135
mdshw5
closed
6 years ago
0
Option for failing if index not found
#134
marcelm
closed
6 years ago
10
Fasta to Bed
#133
atfields
closed
6 years ago
2
Tiny typo: diffent -> different
#132
croth1
closed
6 years ago
2
Recursion error when with bfgz files
#131
arivers
closed
6 years ago
9
Create CODE_OF_CONDUCT.md
#130
mdshw5
closed
6 years ago
0
FastaVariant example not working
#129
daquang
closed
6 years ago
6
`Sequence.gc` methods that consider IUPAC nucleotide ambiguity
#128
mdshw5
opened
6 years ago
0
initial version of spliced sequence retrieval
#127
simonvh
closed
6 years ago
5
Create or load htslib .fai and .gzi index files when using BGZF files
#126
KwatMDPhD
closed
3 years ago
12
BGZF recursion issue
#125
KwatMDPhD
closed
6 years ago
11
bgzipped file does not work
#124
KwatMDPhD
closed
5 years ago
9
Update __init__.py
#123
KwatMDPhD
closed
7 years ago
3
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