Changes for seqmagick¶

0.8.0¶

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]

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]

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

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)

Fix bug in --squeeze
More informative messages in seqmagick primer-trim
Added --alphabet flag to allow writing NEXUS (GH-23)
Exiting without error on SIGPIPE in extract-ids, info (GH-17)
Ambiguities are translated as ‘X’ in –translate (GH-16)
Allowing ‘.’ or ‘-’ as gap character (GH-18)
--name-prefix and --name-suffix no longer create a mangled description (GH-19)
Files owned by another user can be mogrified, as long as they are group writeable (GH-14)
Add backtrans-align subcommand, which maps unaligned nucleotides onto a protein alignment (GH-20)
Allow FASTQ as input to quality-filter
Significantly expand functionality of quality-filter: identify and trim barcodes/primers; report detailed failure information.
Cleanup, additional tests
Add --drop filter to convert and mogrify (GH-24)
Apply current umask when creating files (GH-26)
Support stdin in seqmagick info (GH-27)
Support translating ambiguous nucleotides, if codon translation is unambiguous

Internal reorganization - transformations are converted to partial functions, then applied.
Argument order now affects order of tranformation application.
Change default output format to ‘align’ for TTYs in seqmagick info
Add BioPython as dependency (closes GH-7)
Add primer-trim subcommand
Add option to apply custom function(s) to sequences
Add new filtering options: --squeeze-threshold, --min-ungapped-length --include-from-file --exclude-from-file
Removed seqmagick muscle
Added new subcommand quality-filter
Added new subcommand extract-ids (closes GH-13)
Allow use of ‘-’ to indicate stdin / stdout (closes GH-11)
Add mapping from .phyx to phylip-relaxed (targeted for BioPython 1.58)

Refactoring
Added hyphenation to multi-word command line options (e.g. --deduplicatetaxa -> --deduplicate-taxa)
Add support for .needle, .sff formats
Close GH-4

Initial release