fhcrc/seqmagick

Issues

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

  #95 opened 4 years ago by bowmanjeffs
  1

• Bio.pairwise2 will be deprecated

  #96 opened 2 years ago by lukaszsobala
  4

• TravisCI -> gh actions

  #99 opened 2 years ago by jgallowa07
  0

• nose -> nose2

  #98 opened 2 years ago by jgallowa07
  0

• Error with --reverse-complement: random prefix of letters appended to fastq file name, causing failure to read.

  #94 opened 4 years ago by jsacco1
  1

• FastaWriter for line wrap control broken in Biopython 1.77?

  #93 opened 4 years ago by ressy
  2

• update setup.py

  #90 opened 4 years ago by jgallowa07
  0

• convert from fasta fails on stable biopython (Bio.Alphabet has been removed from Biopython)

  #87 opened 4 years ago by wwood
  2

• Please replace deprecated module Bio.triefind

  #84 opened 5 years ago by tillea
  2

• SeqIO.index does not support gzip files

  #42 opened 5 years ago by crosenth
  2

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

  #81 opened 5 years ago by asttra
  2

• Total length column with the info command

  #57 opened 5 years ago by nr0cinu
  0

• Trim high identity sites/columns from alignment?

  #83 opened 5 years ago by metasoarous
  0

• Translation error with new BioPython

  #79 opened 5 years ago by fungs
  6

• seqmagick with no params gives "KeyError:None"

  #77 opened 5 years ago by tseemann
  0

• installed by pip, while cant show by type seqmagick in the command line

  #80 opened 6 years ago by whiteorchid
  1

• Test suite throws "TypeError: argument of type 'int' is not iterable"

  #73 opened 7 years ago by tillea
  6

• pip3 install preferred over pip3 install

  #78 opened 7 years ago by tseemann
  1

• Mixed error messages and real output on stdout

  #74 opened 7 years ago by fungs
  2

• adding N to the "gap characters"

  #72 opened 7 years ago by dunleavy005
  3

• Obtain the reverse fastq of forward single reads using seqmagick?

  #70 opened 7 years ago by galud27
  0

• Deduplication using seqmagick

  #69 opened 7 years ago by dot4822
  3

• out of date docs still hanging around

  #60 opened 7 years ago by matsen
  9

• Missing paretheses if run setup.py with python 3

  #44 opened 7 years ago by hcraT
  3

• python 3 support?

  #56 opened 7 years ago by wwood
  4

• Please consider updating to support Python >3.x

  #65 opened 7 years ago by fizwit
  1

• issue with Biopython 1.67

  #59 opened 7 years ago by bowmanjeffs
  2

• restore support for bz2 compression

  #66 opened 7 years ago by nhoffman
  0

• Behavior of --squeeze coupled with sequence selection

  #64 opened 8 years ago by metasoarous
  0

• more detailed seqmagick info on specific sequences

  #63 opened 8 years ago by metasoarous
  0

• backtrans-align breaks if any dna seq length isn't a multiple of 3

  #62 opened 8 years ago by metasoarous
  0

• backtrans-align should have an option for sorting sequences for you

  #61 opened 8 years ago by metasoarous
  0

• SIGPIPE problem in Windows

  #58 opened 9 years ago by katieMlyons
  2

• tests not run in setup.py

  #55 opened 10 years ago by wwood
  1

• quality-filter --pct-ambiguous

  #53 opened 10 years ago by crosenth
  1

• push to pypi

  #51 opened 10 years ago by wwood
  1

• convert docs are broken

  #43 opened 10 years ago by matsen
  4

• how to translate into 6 frames ?

  #46 opened 10 years ago by lmanchon
  1

• pip install seqmagick failed

  #50 opened 10 years ago by sjackman
  1

• would fasta comparison fit into the seqmagick framework?

  #49 opened 10 years ago by cswarth
  0

• Transforms relying on `description` attribute fail on NEXUS files

  #47 opened 10 years ago by bcclaywell
  1

• Case insensitive `convert --pattern-replace`

  #38 opened 11 years ago by sjackman
  9

• Request: Make sequence IDs unique

  #40 opened 11 years ago by sjackman
  2

• Anchored --pattern-replace doesn't replace

  #39 opened 11 years ago by sjackman
  2

• backtrans-align: codon:proein length missmatch error message should include sequence name

  #37 opened 11 years ago by metasoarous
  0

• --sample N causes error if number of seqs < N

  #35 opened 11 years ago by nhoffman
  4

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

  #33 opened 12 years ago by wwood
  4

• Support reading and writing compressed files

  #30 opened 12 years ago by cmccoy
  0

• `extract-ids --source-format` is inconsistent

  #29 opened 12 years ago by cmccoy
  0

• backtrans-align docs appear 2x

  #28 opened 13 years ago by matsen
  0