History

v0.6.0 (21st November 2023)

Changed the package name to methlab.

v0.5.0 (13th November 2023)

Added methylation_state to quantify the evidence that regions are unmethylated, CG-only methylated or TE-like methylated.

v0.4.3 (25th October 2023)

Added support for checking methylation in windows for only a subset of chromosomes

v0.4.2 (15th September 2023)

  • Committed docs for CytosineCoverageFile and BismarkSam.

  • Added support for pulling out strand tags from SAM files. This generalises to

    any custom SAM tag.

v0.4.1 (12th September 2023)

  • Fixed install_requires.

  • SAM files now return the SAM flag.

v0.4.0 (12th September 2023)

  • Class to manipulate aligned SAM files from Bismark.

  • Included docs on how to use.

v0.3.0 (8th September 2023)

  • Documentaion for align_fastq_with_plate_positions and CytosineCoverageFile.

v0.2.2 (25th July 2023)

Created a class to import and take apart cytosine coverage files from Bismark.

  • count_reads counts up methylated and unmethylated reads, plus total number of cytosines in each sequence context.

  • methylation_over_features takes series of genome coordinates (from an

    annotation file, for example), pulls out each part of the coverage file and calls count_reads on each.

  • conversion_rate calculates mean methylation on each chromosome

  • methylation_in_windows partitions the genome in to windows of fixed size and

    calls count_reads on each.

0.1.0 (2023-06-29)

  • Initial commit

  • Function align_fastq_with_plate_positions.py` looks up adaptor index positions from bam file names