* Supports Python 3.5+ * Drops support for Python 3.4 * Fix issue: "seqmagick with no params gives KeyError:None" [GH-77] * Fix for Biopython 1.71 dual coding support [GH-76]; also fixes issue: "Translation error with new BioPython" [GH-79] * Send logging to stderr, not stdout [GH-75]
0.7.0
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* Supports Python 3.4+ * Drops support for python 2.7 * requires biopython >= 1.70 * Drops support for bz2 compression [see GH-66] * New option ``convert --sample-seed`` to make ``--sample`` deterministic.
0.6.2
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* New ``quality-filter --pct-ambiguous`` switch [GH-53] * setup.py enforces biopython>=1.58,<=1.66 (1.67 is not compatible) [GH-59] * This is the last release that will support Python 2!
0.6.1
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* Allow string wrapping when input isn't FASTA. [GH-45] * Fix ``--pattern-include``, ``--pattern-exclude``, and ``--pattern-replace`` for sequences without descriptions (e.g., from NEXUS files). [GH-47] * Fix mogrify example. [GH-52]
0.6.0
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* Map ``.nex`` extension to NEXUS-format (--alphabet must be specified if writing) * Use reservoir sampling in ``--sample`` selector (lower memory use) * Support specifying negative indices to ``--cut`` [GH-33] * Optionally allow invalid codons in ``backtrans-align`` [GH-34] * Map ``.fq`` extension to FASTQ format * Optional multithreaded I/O in ``info`` [GH-36] * Print sequence name on length mismatch in ``backtrans-align`` [GH-37] * Support for ``+`` and ``-`` in head and tail to mimick Linux head and tail commands. * Fix scoring for mixed-case sequences in ``primer-trim``. * Fix bug in ``primer-trim`` - failed when sequence had multiple 5' gaps compared to the primer. * Clarify documentation and fix bug in convert/mogrify ``--pattern-replace`` [GH-39] * Support for gzip files in ``seqmagick convert --sort``
0.5.0
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* Change ``seqmagick extract-ids --source-format`` to ``--input-format`` to match other commands (GH-29) * Support gzip- and bzip2-compressed inputs and outputs for most commands (GH-30) * Change default input format for ``sff`` to ``sff-trim``, which respects the clipping locations embedded in each sequence record. * Add ``--details-out`` option to ``seqmagick quality-filter``, which writes details on each read processed. * Match barcode/primer ``seqmagick quality-filter`` against a trie; allows per-specimen barcodes. * Remove ``--failure-out`` option from ``seqmagick quality-filter``. See ``--details-out`` * Raise an error if number of codons does not match number of amino acids in ``seqmagick backtrans-align`` * Add ``--sample`` subcommand (GH-31)