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

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Port Seq.ungap call to Biopython 1.80.

#101 emollier closed 8 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 4 years ago
4
quick patch changing biopython requirement to 1.77

#88 jgallowa07 closed 4 years ago
1
convert from fasta fails on stable biopython (Bio.Alphabet has been removed from Biopython)

#87 wwood closed 4 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