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
#94 - Error with --reverse-complement: random prefix of letters appended to fastq file name, causing failure to read.
Issue -
State: closed - Opened by jsacco1 almost 4 years ago
- 1 comment
#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
#87 - convert from fasta fails on stable biopython (Bio.Alphabet has been removed from Biopython)
Issue -
State: closed - Opened by wwood about 4 years ago
- 2 comments
#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 almost 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
#70 - Obtain the reverse fastq of forward single reads using seqmagick?
Issue -
State: open - Opened by galud27 over 6 years ago
#69 - Deduplication using seqmagick
Issue -
State: closed - Opened by dot4822 over 6 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
#62 - backtrans-align breaks if any dna seq length isn't a multiple of 3
Issue -
State: open - Opened by metasoarous almost 8 years ago
#61 - backtrans-align should have an option for sorting sequences for you
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
#37 - backtrans-align: codon:proein length missmatch error message should include sequence name
Issue -
State: closed - Opened by metasoarous almost 11 years ago
#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
#27 - Feature request: stdin support using '-' character in `seqmagick info`
Issue -
State: closed - Opened by crosenth over 12 years ago
#26 - Files created by {convert,mogrify} don't obey umask
Issue -
State: closed - Opened by cmccoy over 12 years ago
#25 - Feature request: default --[input|output]-format to 'fasta' for stdin and stdout
Pull Request -
State: closed - Opened by nhoffman 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