From 84f800fbcff6a36cef8700621967993b35c47aba Mon Sep 17 00:00:00 2001
From: Emanuel Burgos <eburgos@wisc.edu>
Date: Wed, 16 Jun 2021 11:42:21 -0500
Subject: [PATCH] Final changes for v0.2.1 release (#79)

* Final changes for 0.2.1 release

* Increase version number: 0.2.0 -> 0.2.1

* Add new args of barcode_length and transposon_seq

* Adding barcode_length and transposon_seq arguments

Now the user can define the barcode index length from 4bp - 16bp and provide their own transposon sequence for regex searches as an argument to pyinseq

* Add tests for new args

* Disclaimer of future snakemake version
---
 CHANGELOG.md      | 23 +++++++++++++++++------
 README.md         |  7 +++++++
 mkdocs.yml        |  2 +-
 pyinseq/runner.py |  4 ++--
 4 files changed, 27 insertions(+), 9 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 806cfab..7c25e21 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,15 +1,26 @@
 # Changelog
 
-## [Unreleased]
+## [0.2.1] - 2021-06-02
 ### Fixed
 - `pyinseq` alone brings up the help documentation
-- Small fix to the `three_primeness` calculation.
+- 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+ supported
+- Only Python 3.6 and 3.7 are supported.
+- `screed` module is used for opening/writing fastq files.
+
 ### Added
-- `pyinseq genomeprep` command
-- Added T50 calculation
-- Added progress bar for `demultiplex` function
+- `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
diff --git a/README.md b/README.md
index 38993a9..93e4cf9 100644
--- a/README.md
+++ b/README.md
@@ -2,8 +2,15 @@
 ![Python 3.6](https://img.shields.io/badge/python-3.6-blue.svg)
 ![Python 3.7](https://img.shields.io/badge/python-3.7-blue.svg)
 
+
 # pyinseq
 
+### Disclaimer
+
+A new version of `pyinseq` that works with `snakemake` will be released on `bioconda` in the Summer of 2021
+
+### About
+
 Lightweight package to map transposon insertion sequencing (INSeq) data in
 bacteria.
 
diff --git a/mkdocs.yml b/mkdocs.yml
index a62aba0..d96e3cd 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -1,6 +1,6 @@
 site_name: pyinseq
 theme: cinder
-copyright: 2015-2018 Mark Mandel and Contributors
+copyright: 2015-2021 Mark Mandel and Contributors
 
 nav:
   - Home: index.md
diff --git a/pyinseq/runner.py b/pyinseq/runner.py
index d0869eb..c2b11a1 100644
--- a/pyinseq/runner.py
+++ b/pyinseq/runner.py
@@ -109,12 +109,12 @@ def demultiplex_parse_args(args):
     )
     parser.add_argument(
         "--barcode_length",
-        help="Length of the barcode which is used to demultiplex samples (4 - 16)",
+        help="Length of the barcode which is used to demultiplex samples (4 - 16 nt). Default is 4.",
         default=4,
     )
     parser.add_argument(
         "--transposon_seq",
-        help="Sequence for the transposon that flanks reads",
+        help="Sequence for the transposon that flanks reads. Default is ACAGGTTG.",
         default="ACAGGTTG",
     )
     return parser.parse_args(args)