0.1.1 (2016-07-07)

  • Updated citation.

    Please cite us! <3

  • [PR:ar0ch] Add lowercase matching in GCRatioStrategy

    Fixes ‘feature’ where lowercase letters are ignored by GCRatioStrategy.

0.1.0 (2016-03-08)

  • Goldilocks is published software!


  • -l and -s CLI arguments and corresponding length and stride parameters to Goldilocks constructor now support SI suffixes: K, M, G, T. util module contains parse_si_bp used to parse option strings and return the number of bases for length and stride.

  • Add length and stride to x-axis label of plots.

  • Add ignore_query option to plot to override new default behaviour of plot that only plots points for regions remaining after a call to query.

  • Remove profile function, use plot with bins=N instead.

  • Add binning to plot to reduce code duplication.

  • Add chrom kwarg to plot to allow plotting of a single chromosome across multiple input genomes.

  • Fix support for plotting data from multiple contigs or chromosomes of a single input genome when provided as a FASTA.

  • Add ignore_query kwarg to plot for ignoring the results of a query on the Goldilocks object when performing a plot afterwards.

  • Bins no longer have to be specified manually, use bins=N, this will create N+1 bins (a special 0 bin is reserved) between 0 and the largest observed value unless bin_max is also provided.

  • Bins may have a hard upper limit set with bin_max. This will override the default of the largest observed value regardless of whether bin_max is smaller.

  • Plots can now be plotted proportionally with prop=True.

  • Improve labels for plotting.

  • Reduce duplication of plotting code inside plot.

  • Share Y axis across plot panels to prevent potentially misleading default plots.

  • Reduce duplication of code used for outputting metadata:

  • Add fmt kwarg to export_meta that permits one of:
    • bed

      BED format (compulsory fields only)

    • circos

      A format compatible with the circos plotting tool

    • melt

      A format that will suit import to an R dataframe without the need for additional munging with reshape2

    • table

      A plain tabular format that will suit for quick outputs with some munging

  • Remove print_melt, use export_meta with fmt=melt.

  • Add is_pos_file kwarg to Goldilocks, allows user to specify position based variants in the format CHRtPOS or CHR:POS in a newline delimited file.

  • Changed required idx key to file in sequence dictionaries.

  • Added custom strategy and plotting examples to the documentation.

  • The Goldilocks class is now imported as from goldilocks import Goldilocks.

  • The textwrap.wrap function is used to write out FASTA more cleanly.

  • A serious regression in the parsing of FASTA files introduced by v0.0.80 has been closed.

  • Improved plotting functionality for co-plotting groups, tracks of chromosome has been introduced. Tracks can now be plotted together on the same panel by providing their names as a list to the tracks keyword.

  • reset_candidates allows users to “reset” the Goldilocks object after a query or sort has been performed on the regions.

0.0.82 (2016-01-29)

  • Changed example to use MotifCounterStrategy over removed KMerCounterStrategy.
  • Fix runtime NameError preventing PositionCounterStrategy from executing correctly.
  • Fix runtime NameError preventing ReferenceConsensusStrategy from executing correctly.
  • Add default count track to PositionCounterStrategy to prevent accidental multiple counting issue encountered when couting with the default track.
  • Paper accepted for press!

0.0.81 (2016-01-29)

  • Fix versioning error.

0.0.80 (2015-08-10)

  • Added multiprocessing capabilities during census step.
  • Added a simple command line interface.
  • Removed prepare-evaluate paradigm from strategies and now perform counts directly on input data in one step.
  • Skip slides (and set all counts to 0) if their end_pos falls outside of the region on that particular genome’s chromosome/contig.
  • Rename KMerCounterStrategy to MotifCounterStrategy
  • Fixed bug causing use_and to not work as expected for chromosomes not explicitly listed in the exceptions dict when also using use_chrom.
  • Support use of FASTA files which must be supplied with a samtools faidx style index.
  • Stopped supporting Python 3 due to incompatability with buffer and memoryview.
  • Prevent query from deep copying itself on return. Note this means that a query will alter the original Goldilocks object.
  • Now using a 3D numpy matrix to store counters with memory shared to support multiprocessing during census.
  • Removed StrategyValue as these cannot be stored in shared memory. This makes ratio-based strategies a bit of a hack currently (but still work...)
  • tldr; Goldilocks is at least 2-4x faster than previously, even without multiprocessing

0.0.71 (2015-07-11)

  • Officially add MIT license to repository.

  • Deprecate _filter.

  • Update and tidy examples.py.

  • is_seq argument to initialisation removed and replaced with is_pos.

  • Use is_pos to indicate the expected input is positional, not sequence.

  • Force use of PositionCounterStrategy when is_pos is True.

  • Sequence data now read in to 0-indexed arrays to avoid the overhead of string

    re-allocation by having to append a padding character to the beginning of very long strings.

  • Region metadata continues to use 1-indexed positions for user output.

  • VariantCounterStrategy now PositionCounterStrategy.

  • PositionCounterStrategy expects 1-indexed lists of positions;

    prepare populates the listed locations with 1 and then evaluate returns the sum as before.

  • test_regression2 updated to account for converting 1-index to 0-index when

    manually handling the sequence for expected results.

  • query accepts gmax and gmin arguments to filter candidate regions by the group-track value.

  • CandidateList removed and replaced with simply returning a new Goldilocks.

0.0.6 (2015-06-23)

  • Goldilocks.sorted_regions stores a list of region ids to represent the result of a sorting operation following a call to query.
  • Regions in Goldilocks.regions now always have a copy of their “id” as a key.
  • __check_exclusions now accepts a group and track for more complex exclusion-based operations.
  • region_group_lte and region_group_gte added to usable exclusion fields to remove regions where the value of the desired group/track combination is less/greater than or equal to the value of the group/track set by the current query.
  • query now returns a new Goldilocks instance, rather than a CandidateList.
  • Goldilocks.candidates property now allows access to regions, this property will maintain the order of sorted_regions if it has one.
  • export_meta now allows group=None
  • CandidateList class deleted.
  • Test data that is no longer used has been deleted.
  • Scripts for generating test data added to test_gen/ directory.
  • Tests updated to reflect the fact CandidateList lists are no longer returned by query.
  • _filter is to be deprecated in favour of query by 0.0.7

Beta (2014-10-08)

  • Massively updated! Compatability with previous versions very broken.
  • Software retrofitted to be much more flexible to support a wider range of problems.

0.0.2 (2014-08-18)

  • Remove incompatible use of print

0.0.1 (2014-08-18)

  • Initial package