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@mandel01 mandel01 released this 16 Jun 16:54
· 19 commits to master since this release
v0.2.1
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Learn about vigilant mode.

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.

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