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fhcrc
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seqmagick
An imagemagick-like frontend to Biopython SeqIO
http://seqmagick.readthedocs.org
GNU General Public License v3.0
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push to pypi
#51
wwood
closed
9 years ago
1
pip install seqmagick failed
#50
sjackman
closed
9 years ago
1
would fasta comparison fit into the seqmagick framework?
#49
cswarth
opened
9 years ago
0
Allow filter/replace on IDs without a description.
#48
bcclaywell
closed
9 years ago
5
Transforms relying on `description` attribute fail on NEXUS files
#47
bcclaywell
closed
9 years ago
1
how to translate into 6 frames ?
#46
lmanchon
closed
9 years ago
1
Allowing string wrapping when input isn't FASTA.
#45
matsen
closed
9 years ago
0
Missing paretheses if run setup.py with python 3
#44
hcraT
closed
6 years ago
3
convert docs are broken
#43
matsen
closed
9 years ago
4
SeqIO.index does not support gzip files
#42
crosenth
closed
4 years ago
2
Protparam
#41
omgwtfgames
closed
4 years ago
10
Request: Make sequence IDs unique
#40
sjackman
closed
10 years ago
2
Anchored --pattern-replace doesn't replace
#39
sjackman
closed
10 years ago
2
Case insensitive `convert --pattern-replace`
#38
sjackman
closed
10 years ago
9
backtrans-align: codon:proein length missmatch error message should include sequence name
#37
metasoarous
closed
10 years ago
0
multiprocessing for seqmagick info
#36
crosenth
closed
10 years ago
6
--sample N causes error if number of seqs < N
#35
nhoffman
closed
10 years ago
4
Better handling of invalid codons in `backtrans-align`
#34
cmccoy
closed
11 years ago
1
feature request: --cut from the end of sequences using negative position numbers
#33
wwood
closed
11 years ago
4
--sample argeparse updates
#32
crosenth
closed
11 years ago
1
--sample N
#31
crosenth
closed
11 years ago
0
Support reading and writing compressed files
#30
cmccoy
closed
11 years ago
0
`extract-ids --source-format` is inconsistent
#29
cmccoy
closed
11 years ago
0
backtrans-align docs appear 2x
#28
matsen
closed
12 years ago
0
Feature request: stdin support using '-' character in `seqmagick info`
#27
crosenth
closed
12 years ago
0
Files created by {convert,mogrify} don't obey umask
#26
cmccoy
closed
12 years ago
0
Feature request: default --[input|output]-format to 'fasta' for stdin and stdout
#25
nhoffman
closed
11 years ago
0
Add `--drop`
#24
cmccoy
closed
12 years ago
0
problems writing nexus
#23
gh-owestesson
closed
12 years ago
2
add --relative-to option to extend --cut
#22
nhoffman
closed
12 years ago
5
extend --cut syntax to allow multiple regions
#21
nhoffman
closed
12 years ago
1
Map nucleotides onto a protein alignment
#20
cmccoy
closed
12 years ago
0
`--name-suffix` and `--name-prefix` create unnecessary description
#19
cmccoy
closed
13 years ago
0
seqmagick --ungap doesn't recognize periods as gaps
#18
matsen
closed
13 years ago
2
Commands writing to stdout should exit on SIGPIPE
#17
cmccoy
closed
13 years ago
0
seqmagick should be able to translate DNA to AA with gaps
#16
cmccoy
closed
13 years ago
0
--squeeze returns no records
#15
cmccoy
closed
13 years ago
0
Error mogrifying files owned by another user
#14
cmccoy
closed
13 years ago
1
Add an easy way to extract sequence IDs from sequence file
#13
cmccoy
closed
13 years ago
0
seqmagick info Aligned format incorrect
#12
cmccoy
closed
13 years ago
0
- is not recognized as stdin/stdout in seqmagick convert
#11
habnabit
closed
13 years ago
5
.tre suffix = phylogenetic tree
#10
matsen
closed
13 years ago
1
Add `seqmagick primer-trim`
#9
cmccoy
closed
13 years ago
0
seqmagick should be on PyPI
#8
cmccoy
closed
13 years ago
1
um, INSTALL needs to specify biopython dependency
#7
matsen
closed
13 years ago
1
Add support for custom filtering / modification functions
#6
cmccoy
closed
13 years ago
1
need support for "relaxed" phylip output
#5
nhoffman
closed
13 years ago
3
package organization
#4
nhoffman
closed
13 years ago
3
Quality (etc) information lost when applying transforms
#3
cmccoy
closed
13 years ago
1
Can't run with current biopython
#2
cmccoy
closed
13 years ago
1
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