run.sh

#! /bin/bash 
echo 'Test case examples for bioinformatic toolkits discussed in http://biorxiv.org/content/early/2015/12/25/035360'

echo '```'
echo Software used:
R --version|grep Full 
echo 'ETE3' `ete3 version` 
echo 'ETE2' `python -c 'import ete2; print ete2.__version__'`
echo Dendropy `python -c 'import dendropy; print dendropy.__version__'`
echo BioPython `python -c 'import Bio; print Bio.__version__'`
echo Newick utilities 1.6
echo BioPerl `perl -e 'use Bio::Perl; print Bio::Perl->VERSION."\n"'`
echo PyCogent `python -c 'import cogent; print cogent.__version__'`
echo '```'

echo "###Relevant discussion:"
echo BioPython: https://github.com/biopython/biopython/issues/745
echo
echo Dendropy: https://github.com/jeetsukumaran/DendroPy/issues/53
echo
echo BioPerl: https://github.com/bioperl/bioperl-live/issues/157
echo
echo newick-utilities: https://github.com/tjunier/newick_utils/issues/15
echo 
echo Scikit-bio/PyCogent: https://github.com/biocore/scikit-bio/issues/1355
echo

ete3 view  --attr name support --sin --ss --sbl -i original_tree.png -t test.nw;

echo '## Original tree'
echo '```'
cat test.nw
echo '```'
echo '![ete3](https://github.com/jhcepas/test_branch_support_after_tree_rerooting/blob/master/original_tree.png)' 


echo '## Tree after rooting to X' 

for x in test_ete3.py test_ete2.py test_dendropy.py test_ape.sh test_patched_ape.sh test_newick_utilities.sh test_biopython.py test_bioperl.sh test_pycogent.py
do 
    echo '###' $x
    for ext in .sh .py .pl .R; do  
        base=`echo $x|cut -f1 -d'.'`$ext
        if [[ ! -f $base ]]; then
            continue
        fi
        echo '####' $base
        if [[ $base  =~ .*\.py ]]; then
            echo '```python'
        elif [[ $base  =~ .*\.R ]]; then
            echo '```R'
        elif [[ $base  =~ .*\.sh ]]; then
            echo '```bash'
        elif [[ $base  =~ .*\.pl ]]; then
            echo '```perl'
        else
            echo '```'
        fi
        cat $base
        echo '```'
    done
    echo Resulting newick:
    echo '```'
    ./$x; 
    echo
    echo '```';  
    #./$x|ete3 view --text --attr name support --sin; 
    ./$x |ete3 view  --attr name support --sin --ss --sbl -i $x.png; 
    echo "![$x](https://github.com/jhcepas/test_branch_support_after_tree_rerooting/blob/master/$x.png)"
done