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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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bgzipped file does not work
#124
KwatMDPhD
closed
5 years ago
9
Update __init__.py
#123
KwatMDPhD
closed
7 years ago
3
correct spelling mistake
#122
EdwardBetts
closed
7 years ago
1
keep fasta header lines unmodified, if ranges are provided
#121
tolot27
closed
7 years ago
7
Added basic support for auto reverse-complements
#120
tolot27
closed
7 years ago
5
xargs faidx - copies all input fasta file
#119
TreeT2
closed
7 years ago
2
faidx is killed on large bgzip input file
#118
terrycojones
closed
7 years ago
3
Initialize lastline so we don't fail on empty FASTA.
#117
terrycojones
closed
7 years ago
1
lastline can be referenced before it is assigned to
#116
terrycojones
closed
7 years ago
0
It would be good to have an 0.4.8.5 release
#115
terrycojones
closed
7 years ago
3
Enhancement: Support numpy.int32 and numpy.int64
#114
dburkhardt
closed
7 years ago
1
Proof of concept support for BGZF compressed FASTA files.
#113
terrycojones
closed
7 years ago
10
Use env in the before_script in .travis.yml
#112
terrycojones
closed
7 years ago
1
Allow the use of a key_function in Faidx.build_index
#111
terrycojones
closed
7 years ago
5
Editing FASTA files sporadically does not have effect.
#110
sfbrunner
closed
7 years ago
6
Consolidate long name methods to all use `long_name`
#109
michaelbarton
closed
7 years ago
6
Typo fix for FastaRecord `long_name` method
#108
michaelbarton
closed
7 years ago
4
question about installation
#107
Vivianstats
closed
7 years ago
1
pyfaidx does not successfully install on Travis
#106
mccalluc
closed
7 years ago
7
UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 16813: ordinal not in range(128)
#105
liufengxia99
closed
7 years ago
2
Unicode: ordinal not in range(128)
#104
colindaven
closed
8 years ago
1
Retrieving sequences loses part of the defline
#103
deannachurch
closed
8 years ago
6
Check for malformed .fai entries
#102
mdshw5
closed
7 years ago
1
Force UTF-8 decoding of README.rst on all platforms
#101
nvictus
closed
8 years ago
2
README encoding in setup.py on Python 3
#100
nvictus
closed
8 years ago
1
ValueError: Coordinates start=16572 and end=16571 imply a diffent length than sequence (length 0).
#99
junjieahaha
closed
8 years ago
5
Issue 94
#98
dhauge
closed
8 years ago
1
Issue #96 and Tox configuration
#97
dhauge
closed
8 years ago
5
Faidx.file is not immediately closed if Faidx.__init__ fails when reading/building the index
#96
dhauge
closed
7 years ago
2
Extend Faidx so it can be backed by memory mapped file
#95
dhauge
opened
8 years ago
1
Potential unreleased in Faidx.from_file that can lead to deadlock
#94
dhauge
closed
7 years ago
1
Zero length sequence ranges aren't allowed if 'strict_bounds=True'
#93
dhauge
closed
4 years ago
2
Is the "fetch" function thread safe?
#92
simoncchu
closed
4 years ago
7
warn on old index
#91
brentp
closed
8 years ago
5
--gtf option to read regions from transcript definitions
#90
mdshw5
opened
8 years ago
0
Filter `[:,]` from region string when using UCSC style regions
#89
mdshw5
opened
8 years ago
0
Value Error when loading Fasta File
#88
darencard
closed
8 years ago
2
Check for integer_types instead of int.
#87
jrderuiter
closed
8 years ago
1
Accept integer_types instead of only ints.
#86
jrderuiter
closed
8 years ago
3
Combining with future package results in failing int assertion
#85
jrderuiter
closed
8 years ago
0
Support for indels in FastaVariant class
#84
danielecook
opened
8 years ago
4
FastaIndexingError: Line length of fasta file is not consistent! Inconsistent line found in >MT at line 11.
#83
ghost
closed
8 years ago
5
Fix complement() to work on empty strings, better performance
#82
timodonnell
closed
8 years ago
1
complement() throws exception on empty sequences
#81
timodonnell
closed
8 years ago
1
Orientation attribute is None for Sequence objects
#80
handstad
closed
8 years ago
3
Erroneous end coordinates
#79
handstad
closed
8 years ago
6
Debian packaging
#78
mdshw5
closed
8 years ago
6
Read from bgzip compressed files
#77
danielecook
closed
7 years ago
21
Remove errant print
#76
jeffbhasin
closed
9 years ago
2
Q: number of keys == number of headers?
#75
ChillarAnand
closed
9 years ago
2
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