Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / fhcrc/seqmagick issues and pull requests

#101 - Port Seq.ungap call to Biopython 1.80.

Pull Request - State: closed - Opened by emollier 9 months ago - 1 comment

#100 - added rtd v2 configuration file

Pull Request - State: closed - Opened by jgallowa07 over 1 year ago

#99 - TravisCI -> gh actions

Issue - State: open - Opened by jgallowa07 over 1 year ago

#98 - nose -> nose2

Issue - State: open - Opened by jgallowa07 over 1 year ago

#97 - Removed `primer_trim` module and sub-command

Pull Request - State: closed - Opened by jgallowa07 over 1 year ago - 3 comments

#96 - Bio.pairwise2 will be deprecated

Issue - State: closed - Opened by lukaszsobala almost 2 years ago - 4 comments

#95 - NameError: name 'IUPAC' is not defined in primer-trim.py

Issue - State: open - Opened by bowmanjeffs over 3 years ago

#93 - FastaWriter for line wrap control broken in Biopython 1.77?

Issue - State: closed - Opened by ressy almost 4 years ago - 2 comments

#92 - Adding power support for this package to support arch independent

Pull Request - State: open - Opened by asellappen almost 4 years ago

#91 - added pygtrie to setup

Pull Request - State: closed - Opened by jgallowa07 almost 4 years ago - 1 comment

#90 - update setup.py

Issue - State: closed - Opened by jgallowa07 almost 4 years ago

#89 - Proposal for Biopython 1.78 compatibility

Pull Request - State: closed - Opened by emollier about 4 years ago - 4 comments

#88 - quick patch changing biopython requirement to 1.77

Pull Request - State: closed - Opened by jgallowa07 about 4 years ago - 1 comment

#86 - Replace Biopython trie with pygtrie

Pull Request - State: closed - Opened by nileshpatra over 4 years ago - 2 comments

#85 - Encode hash result in hash_starts_numeric

Pull Request - State: closed - Opened by nileshpatra over 4 years ago - 4 comments

#84 - Please replace deprecated module Bio.triefind

Issue - State: closed - Opened by tillea over 4 years ago - 2 comments

#83 - Trim high identity sites/columns from alignment?

Issue - State: open - Opened by metasoarous over 4 years ago

#82 - version 0.8.0

Pull Request - State: closed - Opened by eharkins almost 5 years ago

#81 - fasta to nexus conversion -- ValueError: Sequences must all be the same length

Issue - State: open - Opened by asttra about 5 years ago - 2 comments

#80 - installed by pip, while cant show by type seqmagick in the command line

Issue - State: closed - Opened by whiteorchid over 5 years ago - 1 comment

#79 - Translation error with new BioPython

Issue - State: closed - Opened by fungs about 6 years ago - 6 comments

#78 - pip3 install preferred over pip3 install

Issue - State: open - Opened by tseemann over 6 years ago - 1 comment

#77 - seqmagick with no params gives "KeyError:None"

Issue - State: closed - Opened by tseemann over 6 years ago

#76 - Fix for Biopython 1.71 dual coding support

Pull Request - State: closed - Opened by peterjc over 6 years ago

#75 - Send logging to stderr, not stdout

Pull Request - State: closed - Opened by peterjc over 6 years ago - 3 comments

#74 - Mixed error messages and real output on stdout

Issue - State: closed - Opened by fungs over 6 years ago - 2 comments

#73 - Test suite throws "TypeError: argument of type 'int' is not iterable"

Issue - State: closed - Opened by tillea over 6 years ago - 6 comments

#72 - adding N to the "gap characters"

Issue - State: open - Opened by dunleavy005 over 6 years ago - 3 comments

#71 - Add Docker and CircleCI

Pull Request - State: closed - Opened by hawkrives over 6 years ago - 1 comment

#69 - Deduplication using seqmagick

Issue - State: closed - Opened by dot4822 almost 7 years ago - 3 comments

#68 - Update README.rst

Pull Request - State: closed - Opened by wangmengbo almost 7 years ago - 1 comment

#67 - Python 3 compatibility

Pull Request - State: closed - Opened by nhoffman almost 7 years ago - 9 comments

#66 - restore support for bz2 compression

Issue - State: open - Opened by nhoffman almost 7 years ago

#65 - Please consider updating to support Python >3.x

Issue - State: closed - Opened by fizwit over 7 years ago - 1 comment

#64 - Behavior of --squeeze coupled with sequence selection

Issue - State: open - Opened by metasoarous almost 8 years ago

#63 - more detailed seqmagick info on specific sequences

Issue - State: open - Opened by metasoarous almost 8 years ago

#60 - out of date docs still hanging around

Issue - State: closed - Opened by matsen almost 8 years ago - 9 comments

#59 - issue with Biopython 1.67

Issue - State: closed - Opened by bowmanjeffs about 8 years ago - 2 comments

#58 - SIGPIPE problem in Windows

Issue - State: open - Opened by katieMlyons over 8 years ago - 2 comments

#57 - Total length column with the info command

Issue - State: closed - Opened by nr0cinu about 9 years ago

#56 - python 3 support?

Issue - State: closed - Opened by wwood about 9 years ago - 4 comments

#55 - tests not run in setup.py

Issue - State: closed - Opened by wwood about 9 years ago - 1 comment

#54 - new pct-ambiguous switch plus test cases

Pull Request - State: closed - Opened by crosenth over 9 years ago
Labels: feature

#53 - quality-filter --pct-ambiguous

Issue - State: closed - Opened by crosenth over 9 years ago - 1 comment
Labels: feature

#52 - Update convert_mogrify.rst

Pull Request - State: closed - Opened by nr0cinu over 9 years ago - 1 comment

#51 - push to pypi

Issue - State: closed - Opened by wwood over 9 years ago - 1 comment

#50 - pip install seqmagick failed

Issue - State: closed - Opened by sjackman over 9 years ago - 1 comment

#49 - would fasta comparison fit into the seqmagick framework?

Issue - State: open - Opened by cswarth over 9 years ago
Labels: feature

#48 - Allow filter/replace on IDs without a description.

Pull Request - State: closed - Opened by bcclaywell over 9 years ago - 5 comments

#47 - Transforms relying on `description` attribute fail on NEXUS files

Issue - State: closed - Opened by bcclaywell over 9 years ago - 1 comment

#46 - how to translate into 6 frames ?

Issue - State: closed - Opened by lmanchon over 9 years ago - 1 comment

#45 - Allowing string wrapping when input isn't FASTA.

Pull Request - State: closed - Opened by matsen almost 10 years ago

#44 - Missing paretheses if run setup.py with python 3

Issue - State: closed - Opened by hcraT almost 10 years ago - 3 comments

#43 - convert docs are broken

Issue - State: closed - Opened by matsen about 10 years ago - 4 comments

#42 - SeqIO.index does not support gzip files

Issue - State: closed - Opened by crosenth about 10 years ago - 2 comments

#41 - Protparam

Pull Request - State: closed - Opened by omgwtfgames over 10 years ago - 10 comments

#40 - Request: Make sequence IDs unique

Issue - State: closed - Opened by sjackman over 10 years ago - 2 comments

#39 - Anchored --pattern-replace doesn't replace

Issue - State: closed - Opened by sjackman over 10 years ago - 2 comments

#38 - Case insensitive `convert --pattern-replace`

Issue - State: closed - Opened by sjackman over 10 years ago - 9 comments

#36 - multiprocessing for seqmagick info

Pull Request - State: closed - Opened by crosenth almost 11 years ago - 6 comments

#35 - --sample N causes error if number of seqs < N

Issue - State: closed - Opened by nhoffman about 11 years ago - 4 comments

#34 - Better handling of invalid codons in `backtrans-align`

Pull Request - State: closed - Opened by cmccoy about 11 years ago - 1 comment

#33 - feature request: --cut from the end of sequences using negative position numbers

Issue - State: closed - Opened by wwood over 11 years ago - 4 comments

#32 - --sample argeparse updates

Pull Request - State: closed - Opened by crosenth over 11 years ago - 1 comment

#31 - --sample N

Pull Request - State: closed - Opened by crosenth about 12 years ago

#30 - Support reading and writing compressed files

Issue - State: closed - Opened by cmccoy about 12 years ago

#29 - `extract-ids --source-format` is inconsistent

Issue - State: closed - Opened by cmccoy about 12 years ago

#28 - backtrans-align docs appear 2x

Issue - State: closed - Opened by matsen over 12 years ago

#26 - Files created by {convert,mogrify} don't obey umask

Issue - State: closed - Opened by cmccoy over 12 years ago

#24 - Add `--drop`

Issue - State: closed - Opened by cmccoy over 12 years ago

#23 - problems writing nexus

Issue - State: closed - Opened by gh-owestesson about 13 years ago - 2 comments

#22 - add --relative-to option to extend --cut

Issue - State: closed - Opened by nhoffman about 13 years ago - 5 comments

#21 - extend --cut syntax to allow multiple regions

Issue - State: closed - Opened by nhoffman about 13 years ago - 1 comment

#20 - Map nucleotides onto a protein alignment

Issue - State: closed - Opened by cmccoy about 13 years ago
Labels: feature

#19 - `--name-suffix` and `--name-prefix` create unnecessary description

Issue - State: closed - Opened by cmccoy about 13 years ago

#18 - seqmagick --ungap doesn't recognize periods as gaps

Issue - State: closed - Opened by matsen about 13 years ago - 2 comments

#17 - Commands writing to stdout should exit on SIGPIPE

Issue - State: closed - Opened by cmccoy about 13 years ago

#16 - seqmagick should be able to translate DNA to AA with gaps

Issue - State: closed - Opened by cmccoy over 13 years ago

#15 - --squeeze returns no records

Issue - State: closed - Opened by cmccoy over 13 years ago

#14 - Error mogrifying files owned by another user

Issue - State: closed - Opened by cmccoy over 13 years ago - 1 comment

#13 - Add an easy way to extract sequence IDs from sequence file

Issue - State: closed - Opened by cmccoy over 13 years ago
Labels: feature

#12 - seqmagick info Aligned format incorrect

Issue - State: closed - Opened by cmccoy over 13 years ago

#11 - - is not recognized as stdin/stdout in seqmagick convert

Issue - State: closed - Opened by habnabit over 13 years ago - 5 comments

#10 - .tre suffix = phylogenetic tree

Issue - State: closed - Opened by matsen over 13 years ago - 1 comment
Labels: feature

#9 - Add `seqmagick primer-trim`

Issue - State: closed - Opened by cmccoy over 13 years ago

#8 - seqmagick should be on PyPI

Issue - State: closed - Opened by cmccoy over 13 years ago - 1 comment

#7 - um, INSTALL needs to specify biopython dependency

Issue - State: closed - Opened by matsen over 13 years ago - 1 comment

#6 - Add support for custom filtering / modification functions

Issue - State: closed - Opened by cmccoy over 13 years ago - 1 comment

#5 - need support for "relaxed" phylip output

Issue - State: closed - Opened by nhoffman over 13 years ago - 3 comments

#4 - package organization

Issue - State: closed - Opened by nhoffman over 13 years ago - 3 comments

#3 - Quality (etc) information lost when applying transforms

Issue - State: closed - Opened by cmccoy over 13 years ago - 1 comment

#2 - Can't run with current biopython

Issue - State: closed - Opened by cmccoy over 13 years ago - 1 comment