From 4f296d19c28d1b7c628eac35922afecc99b76706 Mon Sep 17 00:00:00 2001
From: smaegol <p.krawczyk@ibb.waw.pl>
Date: Fri, 3 Nov 2017 13:35:06 +0100
Subject: [PATCH] minor improvements

---
 PlasFlow.py | 4 ++++
 README.md   | 8 +++++++-
 2 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/PlasFlow.py b/PlasFlow.py
index b8247e4..9eea3d9 100755
--- a/PlasFlow.py
+++ b/PlasFlow.py
@@ -55,11 +55,14 @@
 # srcipt path is required to find the location of models used for classification (script_path/models)
 script_path = os.path.dirname(os.path.realpath(sys.argv[0]))
 
+#if custom models location is given use it
 if(args.models):
     models_path = args.models
 else:
+    #else - expect to find models in the place where PlasFlow was installed
     models_path = script_path + '/models'
 
+#initialize rpy2
 r = robjects.r
 
 # import Biostrings package for kmer quantification
@@ -202,6 +205,7 @@ def predict(self, data):
 
 
 # class for voting classifier
+#based on http://sebastianraschka.com/Articles/2014_ensemble_classifier.html
 class TF_Vote_Classifier:
     """Voting classifier class."""
 
diff --git a/README.md b/README.md
index 7fbd418..1b7e8f2 100644
--- a/README.md
+++ b/README.md
@@ -40,7 +40,7 @@ PlasFlow is a set of scripts used for prediction of plasmid sequences in metagen
 
 ### Conda-based - recommended
 
-Conda is recommended option for installation as it properly manage all dependencies and allows installation without messing with other packages installed. Conda can be used both as the [Anaconda](https://www.anaconda.com/download/), and [Miniconda](https://conda.io/miniconda.html) (which is easier to install and maintain).
+Conda is recommended option for installation as it properly resolve all dependencies (including R and Biostrings) and allows for installation without messing with other packages installed. Conda can be used both as the [Anaconda](https://www.anaconda.com/download/), and [Miniconda](https://conda.io/miniconda.html) (which is easier to install and maintain).
 
 To exclude the possibility of dependencies conflicts its encouraged to create spearate conda environment for Plasflow using command:
 
@@ -62,6 +62,8 @@ PlasFlow can be easily installed as an Anaconda package from my Anaconda channel
 conda install plasflow -c smaegol
 ```
 
+With this command all required dependencies are installed into created conda environment. When installation is finished PlasFlow can be invoked as described in the [Getting started](#getting-started) section.
+
 When you decide to finish your work with PlasFlow, you can simply deactivate current anaconda environment with command:
 
 ```
@@ -113,11 +115,15 @@ to install R Biostrings go to <https://bioconductor.org/packages/release/bioc/ht
 
 PlasFlow is designed to take a metagenomic assembly and identify contigs which may come from plasmids. It outputs several files, from which the most important is a tabular file containing all predictions (specified with `--output` option).
 
+
+
 Options available in PlasFlow include:
 
 - `--input` - specifies input fasta file with assembly contigs to classify [required]
 - `--output` - a name of the tsv file with the tabular output of classification [required]
 - `--threshold` - manually specified threshold for probability filtering (default = 0.7)
+- `--labels` - manually specified custom location of labels file (used for translation from numeric output to actual class names)
+- `--models` - custom location of models used for prediction (have to be specified if PlasFlow was installed using pip)
 
 To invoke PlasFlow on `test.fasta` dataset (available in the test folder) simply: