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Screed 1.0
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@luizirber luizirber released this 06 Apr 21:23
· 5 commits to master since this release
v1.0
34f3459

We are pleased to announce the release of screed 1.0. Screed is a biological sequence parsing and storage/retrieval library for DNA and protein sequences. It's designed to be lightweight and easy to use
from Python.

This version is the first with API compatibility guarantees, following the semantic versioning guidelines.
Most changes are internal or API clarifications, but there is a new shell command for screed functions and an unified function for writing FAST{A,Q} records.

Documentation is available at http://screed.readthedocs.org/en/v1.0

New items of note:

  • New shell commands for common screed operations:
    • db for database creation (screed db <filename>)
    • dumping FAST{A,Q} records from a db (screed dump_fasta <db> <output> and screed dump_fastq <db> <output>). #55 @luizirber
  • Remove \*_Writer classes and unify record writing in the write_fastx function. #53 @standage
  • We now use pytest as a test runner, codecov for code coverage, and a simplified changelog format. #50 #49 #59 @luizirber @standage

Other bugs fixed/issues closed:

  • Fix reverse complement problems for Python 2.7. #47 @ctb
  • Fix operator comparison. #48 @luizirber
  • Update tests & constrain behavior for screed Records. #54 @ctb
  • Allow sqlite3 import to fail. #56 @ctb
  • Cleanup user docs and code. #62 #57 @standage
  • Simplify use of 'open' internally. #65 @ctb

Known Issues

These are all pre-existing

  • Screed does not support gzip file streaming. This is an issue with Python 2.x and will likely not be fixed in future releases. This is being tracked in dib-lab/khmer#700

  • Screed is overly tolerant of spaces in fast{a,q} which is against spec. This is being tracked in dib-lab/khmer#108

Contributors

@luizirber *@standage @ctb *@betatim

* Indicates new contributors

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