0.3.2

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

[0.3.1] - 2021-07-14

Fixed

• File links in README are now compatible with PyPI

Added

• Pyinseq logo for documentation

0.3.0: Snakemake and conda compatibility, updated documentation, code refactoring

[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

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. These parameters can be edited, see below.

Changed

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

Added

• pyinseq genomeprep subcommand allows the user to check GenBank files before a full run, and also enables the user to perform a standalone preparation of the .fasta and .ftt feature table files from the GenBank file.
• 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.
• 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.

Future

This is the last version before a new snakemake-based workflow to be available on bioconda. The core code will not change, but the new execution will be faster and more modular to enable greater customization.

0.2.0

Added:

• Documentation hosting at 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.

0.1.1

Pipeline works and recreated most of the features from previous Perl pipeline.

The core demultiplexing is slow and will likely be removed in future versions (or will be an optional step rather than required to run the analysis).

Needs additional tests.

Change from v0.1 to address PyPI issues.

0.1

Pipeline recreates most of the features from previous Perl pipeline.

The core demultiplexing is slow and will likely be removed in future versions (or will be an optional step rather than required to run the analysis).

Needs additional tests.