Update readme and add instructions for installation

README.md

@@ -1,30 +1,64 @@
-rootstrap.py: A script to calculate the rootstrap support values for all the branches
+`rootstrap.py`: A script to calculate the rootstrap support values for all the branches
 
 Syntax:
 
-rootstrap.py \<tree file> \<bootstrap trees file> \<is rooted> \<outgroup file>
+```bash
+rootstrap.py <tree file> <bootstrap trees file> <is rooted> <outgroup file>
 
-\<treefile> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  The tree file where you want to calculate the rootstrap support values in Newick format (e.g. tree.treefile).<br />
- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; The tree can be rooted or unrooted.
+<treefile>                     The tree file where you want to calculate the rootstrap support values in Newick format (e.g. tree.treefile). 
+                               The tree can be rooted or unrooted.
 
-\<bootstrap trees file>  All the bootstrap trees in Newick format.<br /> 
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; For example: .ufboot file from IQ-TREE (tree.ufboot)
+<bootstrap trees file>         All the bootstrap trees in Newick format. 
+                               For example: .ufboot file from IQ-TREE (tree.ufboot)
 
-\<is rooted> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;  Are the ML tree and the boostrap trees rooted or not.<br /> 
- &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; True - The trees assumed to be rooted and no outgroup taxa infromation is required <br /> 
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; False - The trees assumed to be unrooted and outgroup taxa infromation is required <br /> 
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; (default: True)
+<is rooted>                    Are the ML tree and the boostrap trees rooted or not. 
+                               True - The trees assumed to be rooted and no outgroup taxa infromation is required  
+                               False - The trees assumed to be unrooted and outgroup taxa infromation is required  
+                               (default: True)
 
-\<outgroup file> ;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;  outgroup taxa in Nexus format. <br /> 
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; The outgroup block can be part of the alignment (e.g. OG_File1.nex) file or in a separate file (e.g. OG_File2.nex)
+<outgroup file>                outgroup taxa in Nexus format. 
+                               The outgroup block can be part of the alignment (e.g. OG_File1.nex) file or in a separate file (e.g. OG_File2.nex)
+```
 
 -------------------------------------------------------------------------------------
-rBED_rSED.py: A script to calculate the root Branchlength Error Distance (rBED) and the root Split Error Distance (rSED)
+`rBED_rSED.py`: A script to calculate the root Branchlength Error Distance (rBED) and the root Split Error Distance (rSED)
 
 Syntax:
 
-rBED_rSED.py \<tree file>
+```bash
+rBED_rSED.py                   <tree file>
 
-\<treefile> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  The tree file (rooted tree only in Newick format) where you want to calculate rBED and rSED values.
+<treefile>                     The tree file (rooted tree only in Newick format) where you want to calculate rBED and rSED values.
+```
 
 Note: In order to calculate rBED and rSED values, the true root should be known (or assumed to be known) in advance.
+
+## Installation
+
+For running the scripts in this repository you will need Python 3, and the dependencies
+listed in `requirements.txt`.
+
+It is recommended to use a virtual environment to avoid complications with system
+dependencies and Python.
+
+For users that prefer `pip`, the following should work assuming you have Python 3
+`python` and `pip` in your command line `$PATH` (if using an older OS, you may still
+have `python3` and `pip3`, so just use those commands instead).
+
+```bash
+$ python -m venv venv             # create a virtual environment called venv with pip
+$ source venv/bin/activate        # load the virtual environment, note the change in some shells displaying the venv name
+(venv) $ pip install -r requirements.txt
+# ... it should take a few minutes to download dependencies from PYPI.org and install in your venv (not in your OS Python modules)
+(venv) $ python rootstrap.py 
+Error: Please provide the ML tree file and the bootstrap trees file
+(venv) $ python rBED_rSED.py 
+Error: Please provide the rooted ML tree file
+```
+
+If you had a similar output to the commands above, your installation worked successfully.
+Have a read at the command syntax instructions to use the scripts.
+
+For Conda users, follow their instructions for [managing environments](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html)
+and just run `pip`. Alternativelly, you can consult [Conda Forge](https://conda-forge.org/)
+searching for equivalent packages and installing them via `conda install $package-name`.

requirements.txt

@@ -0,0 +1,4 @@
+ete3==3.1.*
+dendropy==4.4.*
+biopython==1.78
+six==1.15.*

rootstrap.py

@@ -49,7 +49,7 @@ def all_possible_roots(treefile):
                 raise SystemExit('Error: you have unrooted trees. please deactivate the is_rooted flag and provide outgroup taxa file in Nexus format')
     return roots, sameTree
 
-def caluclate_rootstrap(treeFile, bootFile, is_rooted, out_group):
+def calculate_rootstrap(treeFile, bootFile, is_rooted, out_group):
     '''
     input:
         treeFile: rooted tree in newick format (.treefile in IQ-TREE)
@@ -64,7 +64,7 @@ def caluclate_rootstrap(treeFile, bootFile, is_rooted, out_group):
     trees = []
     polyphyly = 0
     if not is_rooted:
-        if out_group == None:
+        if out_group is None:
             raise SystemExit('Error: Please provide outgroup taxa in Nexus format')
         ML_tree = Tree(treeFile)
         nex = Nexus.Nexus() 
@@ -104,14 +104,13 @@ def caluclate_rootstrap(treeFile, bootFile, is_rooted, out_group):
         ML_tree.write(outfile=rootedMLtree) #write the rooted tree with ingroup taxa only to a file
 
     else:
-        ML_tree = Tree(treeFile)
         with open(bootFile, 'r') as f:
             for tree in f:
                 t = Tree(tree)
                 boottrees.append(t.write(format=9))
 
     N_boottrees = len(boottrees)
-    booted = [(g[0], len(list(g[1]))) for g in ite.groupby(boottrees)] #a list of all unique bootstrap trees with thier number of occurrence
+    booted = [(g[0], len(list(g[1]))) for g in ite.groupby(boottrees)] #a list of all unique bootstrap trees with their number of occurrence
     boottrees = []
     for b in booted:
         t2 = Tree(b[0])
@@ -192,7 +191,7 @@ def rootstrap():
             out_group = sys.argv[4]
     elif len(sys.argv) > 5:
         raise SystemExit('Error: too many arguments')
-    print('Note: ingroup taxa are not monophyletic in {} bootstrap trees\n'.format(caluclate_rootstrap(sys.argv[1], sys.argv[2], is_rooted, out_group)))
+    print('Note: ingroup taxa are not monophyletic in {} bootstrap trees\n'.format(calculate_rootstrap(sys.argv[1], sys.argv[2], is_rooted, out_group)))
 
 if __name__ == '__main__':
     rootstrap()