Changelog

Additions

• sequence.io.fastq.FastqFile for reading and writing FASTQ files
  • Dictionary-like usage
  • Support for sequence and quality scores
  • Different offsets for quality scores are available
• database.entrez.fetch_single_file() has overwrite parameter
  • By default the file is not downloaded, if a file with the same name already exists
• application.blast.BlastWebApp have set_entrez_query() and set_max_results() methods for more customization
• reverse_complement() method for sequence.AnnotatedSequence
  • Creates the reverse complement strand for both the sequence and the features

Changes

• sequence.io.fastq.FastaFile behaves properly like a dictionary
  • Inherits MutableMapping
  • Iteration yields keys (header strings) only, instead of a key-value tuple
• SciPy is required for building the documentation
• sequence.Feature and sequence.Location are immutable and hashable
  • sequence.Location objects in sequence.Feature are stored as set
  • sequence.Feature objects in sequence.Annotation are stored as set

Fixes

• Doctests as part of the unit tests
  • Corrected erroneous docstrings
• Index checks for sequence.Annotation and sequence.AnnotatedSequence
• sequence.io.fasta.get_sequence() and sequence.io.fasta.get_sequences() can read lower case sequences
• // is correctly propagated to sequence.io.genbank.GenBankFile in sequence.io.genbank.MultiFile