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Changelog

[0.3.1] - 2024-10-14

Added

  • Added an option to report the full path of the URL of files if the URL type is local.

Fixed

  • Fixed a bug in the seqspec file with the flag “-f paired” that was causing it to not list out all of the files correctly.

[0.3.0] - 2024-10-10

Added

  • Added typing hints to many Assay and Region functions
  • Added 'k key to seqspec info to display one of meta for metadata, sequence_spec for sequence spec, and library_spec for library spec
  • Added -f format to seqspec info to enable multiple formats for displaying info
  • Added support for 0 length regions in the specification
  • Added ability to modify reads using seqspec modify
  • seqspec init now accepts read information
  • Added templates and updated documentation to myst, website
  • Added new examples (e.g., dogmaseq-dig)
  • Added File object to Read
  • Added SeqKit, SeqProtocol, LibKit, and LibProtocol attributes
  • Added option to specify multiple SeqKit, SeqProtocol, LibKit, LibProtocol for each modality
  • Added name validation against known list of SeqKit, SeqProtocol, LibKit, LibProtocol
  • Added new attributes to Onlist object (Onlist now contains a File object):
    • filetype
    • filesize
    • url
  • Added “file_id” to the File object
  • Added seqspec file command to return the list of files in the spec as paired across reads or interleaved
  • Added seqspec upgrade hidden feature to upgrade v0.2.x seqspec files to v0.3.0.

Changed

  • Updated seqspec index to read strands for chromap
  • Updated seqspec split to correctly split sequence_spec
  • Modified seqspec string to use min_len instead of max_len to accommodate nanopore reads
  • Updated documentation on how to propose new vocabulary
  • Modified the internals of seqspec onlist to manage saving the joined onlist to the -o location when specified (otherwise saves to path where spec lives).
  • Renamed “location” to “urltype” in Onlist object
  • Replaced -r with -i id type for all functions (deprecated -r)
  • Multiple seqspec commands now require the addition of a -s selector [read, region, file]
  • seqspec index can now take in reads, regions, or files and index
  • seqspec modify can now add files to the template
  • Updated splitseq template

Fixed

  • Fixed seqspec onlist functionality
  • Fixed error enumeration in seqspec check

Removed

TODO:

  • Remove lib_struct
  • Remove parent_id

Breaking Changes

  • File elements are now required in Read objects and Onlist objects in version 0.3.0

[0.2.0] - 2024-04-17

Changed

  • seqspec index uses primer and max length of of supplied Read
  • assay_spec renamed library_spec
  • Reorganize specification document
  • Move contribution guidelines from SPECIFICATION.md to CONTRIBUTION.md
  • Move example Regions from SPECIFCATION.md to seqspec/docs/regions
  • seqspec index defaults to indexing reads, --region indexes regions
  • Change descriptors of attributes assay_id, doi
  • Assay attribute assay changed to assay_id
  • Read attribute read_name changed to name
  • Assay attribute publication_date changed to date
  • Assay attribute sequencer changed to sequence_protocol
  • Assay function get_modality changed to get_libspec
  • Region function update_attr uses the max_len to generate random and onlist sequence lengths instead of min_len
  • get_region_by_type changed to get_region_by_region_type to disambiguate between region_type and sequence_type
  • seqspec onlist (by default) searches for onlists in the Regions intersected by the Read passed to -r.
  • Support older versions of matplotlib by handling the spines[["top", "bottom"...]] structure
  • Increase the number of Xs in the random region to match max_len for validation
  • Update seqspec print command to use the replacement assay_id attribute instead of assay
  • Implement downloading onlists via URLs and transparently decompress gzip files
  • Change read_list function to take the onlist object for handling local and remote files
  • Added onlist argument to specify combined barcode list file format (kallisto’s multi-file format and default cartesian product format)

Added

  • Added sequence_spec in the Assay object
  • Added Read object in the sequence_spec object
  • Added sequence_spec to the seqspec json schema
  • Added Read object to specification document
  • Added Read generator to website GUI
  • Added pattern matching to date in Assay (expected date format: DAY MONTH YEAR, where day is one or two numbers, month is the full named month starting with a Capital letter and year is the full year)
  • Added library_kit to Assay object (kit that adds seq adapters)
  • Added library_protocol to Assay object (library that generates insert)
  • Added sequence_kit to Assay object
  • Added website to view example seqspec objects
  • Added get_seqspec to assay returns sequence structure for a given modality
  • Added multiple checks to seqspec check
    • check read modalities exist in assay modalities
    • check primer ids from seqspec are unique and exists as region ids in libspec
    • check that the primer id exists as an atomic region (currently a strong assumption that may be relaxed in the future)
    • check properties of multiple sequence types
      • fixed and regions not null incompatible
      • joined and regions null incompatible
      • random and regions not null incompatible
      • random must have sequence of all X’s
      • onlist and onlist property null incompatible
    • check that the min len is less than or equal to the max len
    • check that the length of the sequence is between min and max len
    • Note a strong assumption in seqspec print is that the sequence have a length equal to the max_len for visualization purposes
  • Added RegionCoordinate object that maps Region min/max lengths to 0-indexed positions
  • seqspec onlist searches for onlists in a Region based on --region flag
  • Added type annotations for join_onlists to clarify it needs a list of Onlist objects
  • Added minimal tests for RegionCoordinate, project_regions_to_coordinates, run_onlist_region, run_onlist_read, and seqspec print functions
  • Added list of options to CLI for -f FORMAT within seqspec onlist and seqspec print
  • Added -s SEQTYPE to seqspec print to disambiguate printing sequence, library, or libseq objects. TODO wrap seqspec info into seqspec print -f info.
  • Added -s SPECOBJECT to seqspec onlist. Specify specific object read, region, or region-type for finding the onlist.
  • Added fetching ability for seqspec onlist from remote with IGVF credentials (credit to detrout)

Removed

TODO:

  • Remove lib_struct
  • Remove parent_id

Fixed

  • Sequencing overlapping pairs now supported
  • seqspec check correctly handles sequences lengths longer than the stated min/max range
  • Fixed test for project_regions_to_coordinates
  • Get the test of seqspec check working again by updating the schema for the refactored example specification YAML files and mocking fastq and barcode files
  • Only return the onlist filename if it’s a local file, downloading remote lists when needed
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