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Releases: mdshw5/pyfaidx

v0.3.4

13 Feb 19:28
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New in version 0.3.4:

  • --delimiter option for cli script and split_char argument for Fasta
    and Faidx

v0.3.3

13 Feb 19:28
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New in version 0.3.3:

  • --split-files option writes each returned sequence to an individual
    file. Names are generated based on the sequence name and region
    coordinates.
  • --stats option prints the name and sequence length for each entry,
    suitable for use as a UCSC-style
    chrom.sizes
    file.
  • Sequence longname attribute allows access to "chr:start-end
    (complement)" formatted names

v0.3.2

13 Feb 19:28
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New in version 0.3.2:

  • Fasta getitem no longer initializes new FastaRecord classes
  • Faidx read_ahead attribute implementaion avoids unnecessary disk
    hits (#34)

v0.3.1

13 Feb 19:29
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New in version 0.3.1:

  • Fasta can now accept an integer index in addition to string keys.

v0.3.0

13 Feb 19:29
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New in version 0.3.0:

  • FastaRecord now works as a line-based iterator
    (#30)
  • Added MutableFastaRecord class that allows same-length in-place
    replacement for FASTA
    (#29)

v0.2.9

13 Feb 19:32
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New in version 0.2.9:

  • Added read-ahead buffer for fast sequential sequence access
    (#26)
  • Fixed a condition where as_raw parameter was not respected
    (#27)

v0.2.8

13 Feb 19:32
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  • Small internal refactoring

v0.2.7

13 Feb 19:32
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New in version 0.2.7:

  • Faidx and Fasta strict_bounds bounds checking logic is more correct
  • Fasta default-seq parameter now works
  • CLI script faidx now takes a BED file for fetching regions from a
    fasta

v0.2.6

13 Feb 19:32
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New in version 0.2.6:

  • Faidx no longer has raw_index attribute or rebuild_index method
    (reduce memory footprint)
  • Faidx index memory usage decreased by 31-40%
  • .fai creation is streaming, performance increase for very large
    indices
  • Possible speed regression when performing many small queries using
    Fasta class

v0.2.5

13 Feb 19:32
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New in version 0.2.5:

  • Fasta and Faidx can take default-seq in addition to as_raw,
    key_function, and strict_bounds parameters.
  • Fixed issue #20
  • Faidx has attribute raw_index which is a list representing the fai
    file.
  • Faidx has rebuild_index and write_fai functions for building and
    writing raw_index to file.
  • Extra test cases, and test cases against Biopython SeqIO