fhcrc seqmagick issues - Githubissues

fhcrc / seqmagick

An imagemagick-like frontend to Biopython SeqIO

http://seqmagick.readthedocs.org

GNU General Public License v3.0

113 stars 22 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Port Seq.ungap call to Biopython 1.80.

#101 emollier closed 7 months ago
1
added rtd v2 configuration file

#100 jgallowa07 closed 1 year ago
0
TravisCI -> gh actions

#99 jgallowa07 opened 1 year ago
0
nose -> nose2

#98 jgallowa07 opened 1 year ago
0
Removed `primer_trim` module and sub-command

#97 jgallowa07 closed 1 year ago
3
Bio.pairwise2 will be deprecated

#96 lukaszsobala closed 1 year ago
4
NameError: name 'IUPAC' is not defined in primer-trim.py

#95 bowmanjeffs opened 3 years ago
0
Error with --reverse-complement: random prefix of letters appended to fastq file name, causing failure to read.

#94 jsacco1 closed 3 years ago
1
FastaWriter for line wrap control broken in Biopython 1.77?

#93 ressy closed 3 years ago
2
Adding power support for this package to support arch independent

#92 asellappen opened 3 years ago
0
added pygtrie to setup

#91 jgallowa07 closed 3 years ago
1
update setup.py

#90 jgallowa07 closed 3 years ago
0
Proposal for Biopython 1.78 compatibility

#89 emollier closed 3 years ago
4
quick patch changing biopython requirement to 1.77

#88 jgallowa07 closed 3 years ago
1
convert from fasta fails on stable biopython (Bio.Alphabet has been removed from Biopython)

#87 wwood closed 3 years ago
2
Replace Biopython trie with pygtrie

#86 nileshpatra closed 4 years ago
2
Encode hash result in hash_starts_numeric

#85 nileshpatra closed 4 years ago
4
Please replace deprecated module Bio.triefind

#84 tillea closed 4 years ago
2
Trim high identity sites/columns from alignment?

#83 metasoarous opened 4 years ago
0
version 0.8.0

#82 eharkins closed 4 years ago
0
fasta to nexus conversion -- ValueError: Sequences must all be the same length

#81 asttra opened 4 years ago
2
installed by pip, while cant show by type seqmagick in the command line

#80 whiteorchid closed 5 years ago
1
Translation error with new BioPython

#79 fungs closed 4 years ago
6
pip3 install preferred over pip3 install

#78 tseemann opened 6 years ago
1
seqmagick with no params gives "KeyError:None"

#77 tseemann closed 4 years ago
0
Fix for Biopython 1.71 dual coding support

#76 peterjc closed 6 years ago
0
Send logging to stderr, not stdout

#75 peterjc closed 6 years ago
3
Mixed error messages and real output on stdout

#74 fungs closed 6 years ago
2
Test suite throws "TypeError: argument of type 'int' is not iterable"

#73 tillea closed 6 years ago
6
adding N to the "gap characters"

#72 dunleavy005 opened 6 years ago
3
Add Docker and CircleCI

#71 hawkrives closed 6 years ago
1
Obtain the reverse fastq of forward single reads using seqmagick?

#70 galud27 opened 6 years ago
0
Deduplication using seqmagick

#69 dot4822 closed 6 years ago
3
Update README.rst

#68 wangmengbo closed 6 years ago
1
Python 3 compatibility

#67 nhoffman closed 6 years ago
9
restore support for bz2 compression

#66 nhoffman opened 6 years ago
0
Please consider updating to support Python >3.x

#65 fizwit closed 6 years ago
1
Behavior of --squeeze coupled with sequence selection

#64 metasoarous opened 7 years ago
0
more detailed seqmagick info on specific sequences

#63 metasoarous opened 7 years ago
0
backtrans-align breaks if any dna seq length isn't a multiple of 3

#62 metasoarous opened 7 years ago
0
backtrans-align should have an option for sorting sequences for you

#61 metasoarous opened 7 years ago
0
out of date docs still hanging around

#60 matsen closed 6 years ago
9
issue with Biopython 1.67

#59 bowmanjeffs closed 6 years ago
2
SIGPIPE problem in Windows

#58 katieMlyons opened 8 years ago
2
Total length column with the info command

#57 nr0cinu closed 4 years ago
0
python 3 support?

#56 wwood closed 6 years ago
4
tests not run in setup.py

#55 wwood closed 9 years ago
1
new pct-ambiguous switch plus test cases

#54 crosenth closed 9 years ago
0
quality-filter --pct-ambiguous

#53 crosenth closed 9 years ago
1
Update convert_mogrify.rst

#52 nr0cinu closed 9 years ago
1