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CHANGELOG.md

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v0.4.0 (2021-10-22)

  • Change the structure of renaming config in TOML.
    • We no longer use "attribute_value = ..."
  • Simplify internals of genbank-to-ddbj.
  • Change compare-ddbj to always count items as multiset elements.
  • Accept case variants in feature/qualifier names.
  • Add TOPOLOGY feature if Is_circular=true exists in source feature
    • Add handling of origin-spanning features in circular genome
  • Merge exons with their parent if its type is *_segment, *_region, or *RNA*.
  • Add new renaming rule: Replace a certain qualifier (key, value) with another
    • This enables the replacement: /exception="ribosomal slippage" --> /ribosomal_slippage.
  • Add the renaming /genome="mitochondrion" -> /organelle="mitochondrion" to the default config
  • Enforce single value to /gene if it has multiple. Put the rest to /gene_synonym.
  • Do not add partial markups (< or >) if /pseudo or /pseudogene exist.
  • Change start codons to ATG only when the genetic code is 1 (/transl_table=1).
  • Do not add assembly_gap if the gap is < 10bp long.
  • Join features if /ribosomal_slippage exists.
  • Copy qualifiers /gene and /gene_synonym to children if a gene feature has them.
  • Add an renaming to /organelle, /host, /sub_strain, /plasmid to the default config
  • Fix a bug in DDBJ parser used in evaluation
    • It gave wrong position when location string is digits.
  • Add preliminary handling of "between-position" location like 138683^138684
    • Without BetweenPosition because Bio.SeqIO.parse() creates FeatureLocation instead.
  • Fix representation of a single-position location with a partial markup (form <100..100,200..300 to <100,200..300).
  • Fix missing FASTA entries that are absent in GFF3
    • Respect the entry order in GFF3 (if provided), and append the only-in-FASTS entries.

v0.3.0 (2021-10-12)

  • Add genbank-to-ddbj for Genbank → DDBJ conversion
  • Add compare-ddbjs for comparing two DDBJ annotations for evaluation
  • Add a non-SO wild items to the default config for feature and qualifier names
  • Update the default config: replace hyphens in qualifier keys with underscores.
  • Fix: Respect feature-wise /transl_table value than the globally-set one.
  • Fix an error when joined features have .sub_features
  • Fix [source] in metadata not used when "source" feature exists in a entry
  • Change not to join features directly under "gene"
  • Fix the default config for feature and qualifier names around /pseudo
  • Fix a bug getting incorrect codon when CompoundLocation has a part < 3bp.
  • Fix start codon detection: no longer change /codon_start value even when !=1
  • Fix stop codon detection
    • consider stop codon does not exists whenever the length (after subtraction by "phase") is not a multiple of 3.

v0.2.4 (2021-10-04)

  • Expand the default config for feature and qualifier names
    • Now based on Sequence Ontology
  • Create bgzip file as a new file, rather than replacing existing FASTA file

v0.2.3 (2021-09-30)

  • Switch to pysam and samtools to index FASTA (called faidx)
    • No longer creates sqlite3 database when reading FASTA
  • Minor fixes

v0.2.2 (2021-09-30)

  • Rename the CLI option from --rename_setting to --config_rename
  • Rename the CLI option form --filter_setting to --config_filter
  • Update the feature-qualifier config for renaming
  • Minor bugfixes

v0.2.1 (2021-09-28)

  • Add the CLI option --version

v0.2.0 (2021-09-28)

  • Improve memory usage when reading a large FASTA file
  • Add CLI options: --rename_setting and --filter_setting to load custom settings
  • Fix locations with inequalities '<' and '>' when start/stop codons are absent
  • Fix a critical bug not inserting source properly
  • Fix a critical bug missing subfeatures in certain cases
  • Fix a critical bug ocassionally getting mRNA's ID wrong.
  • Update the translate-feature renaming table
  • Update the translate-feature pair filtering
  • Add CLI tool: normalize-entry-names for renaming IDs in DDBJ annotation file
  • Many bugfixes

v0.1.1 (2021-09-14)

  • Initial release to PyPI