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CHANGELOG.md

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Changelog

[0.3.2] - 2022-05-16

Fixed

  • Fixed bug in generation of the summary_gene_table.txt file
  • Fixed Travis CI link in README.md
  • Added instructions for mamba installation, which is now required for snakemake

Changed

  • Python version supported: 3.7, 3.8 (dropped support for 3.6)
  • Updated installation instructions

Removed

  • Removed conda package for pyinseq; will rely on installation via pip from PyPi or GitHub

[0.3.1] - 2021-07-14

Fixed

  • File links in README are now compatible with Pypi

Added

  • Pyinseq logo for documentation

[0.3.0] - 2021-07-12

Fixed

  • Refactor demultiplex.py for readability and faster execution
  • Logger is now compatible with snakemake logging module
  • Fixed small parsing bugs in gbk_convert.py

Changed

  • Remove third-party folder which contained bowtie executables (now bowtie is installed via conda or manually)
  • file paths are now handled by pathlib
  • New settings class that is compatible with snakemake
  • The map_reads script is now a stand-alone script
  • Settings class which is used by snakemake and pyinseq
  • Pyinseq and snakemake now use pathlib for handling file paths
  • Removed readthedocs website (documentation is now in the README.md; no longer using ReadTheDocs)
  • Removed docs/
  • Removed third-party/

Added

  • Snakemake can now execute workflows using Snakefile in pyinseq
  • Additional Snakefiles for genomeprep and demultiplex of pyinseq
  • Conda virtual environment files that allow conda to install bowtie software during runtime
  • Parser.py script for parsing command-line arguments
  • Include '--test' option for running pytest on pyinseq
  • New pytests for testing workflows in pyinseq
  • Pyinseq will now summarize sample information and snakemake output
  • New user guide for pyinseq

[0.2.1] - 2021-06-02

Fixed

  • pyinseq alone brings up the help documentation
  • Small fix to the three_primeness calculation. A minimum of 3 reads is now required per site, and a Left:Right max read ratio of 10-fold to be tallied.

Changed

  • Only Python 3.6 and 3.7 are supported.
  • screed module is used for opening/writing fastq files.

Added

  • pyinseq genomeprep subcommand will prepare genome files for pyinseq run. Also checks GenBank files before running.
  • Added T50 calculation for sites files.
  • Added progress bar for demultiplex function and for writing reads to sample files.
  • test_script.py now compares directories and files from pyinseq runs to the expected output.
  • Parameter --min_counts: minimum number of reads at a site required to be tallied. Default is 3
  • Parameter --max_ratio: max ratio allowed between left and right reads around a TA insertion site. Default is 10-fold.
  • Parameter --transposon_seq: define transposon sequence that is found at end of reads to help in demultiplexing. Default is ACAGGTTG
  • Parameter --barcode_length: length of barcode index used to demultiplex reads into samples, allows for 4 - 16 nt. Default is 4.
  • Parameter --gff3: enables pyinseq to write gff3 version of genome files.

[0.2.0] - 2017-07-16

Added

  • Documentation hosting http://pyinseq.readthedocs.io/.
  • pyinseq demultiplex command (including --notrim option).
  • Improved logging of messages during the run.
  • log.txt file to record log output to file.

[0.1.0] - 2016-12-13

Added

  • Initial release.
  • pyinseq command demultiplexes and maps samples.
  • Automated testing using pytest, on TravisCI