Making trees from distances.
Also, distance format conversion (phylip, etc)
git clone [email protected]:lskatz/dists2trees.git
export PATH=$PATH:$(realpath dists2trees/scripts)This package depends on
- perl
- gotree
- quicktree
Usage: diststree.pl [options] < infile > outfile.newick
--algorithm quicktree|rapidnj Default: quicktree
--check Check for all dependencies and then exit
--numcpus default: 1
--tempdir default: a temporary directory that will be deleted.
If provided, then the tempdir will not be deleted.
--help This useful help menu
Usage: dists2.pl [options] < infile > outfile
--informat FORMAT The input format. Default: tsv
--outformat FORMAT The output format. Default: stsv
--help This useful help menu
FORMAT can be: tsv, stsv, matrix, or phylip
where tsv is a three column format of sample1 sample2 distance
and stsv is a tsv file where the samples are sorted (`sort -k1,2n`)
and matrix is a matrix of distances, tab separated, with a header of samples and a first column naming the sample. The first row of the first column needs to have a value but is not read.
and phylip is a standard format of distances
Some optimizations have been made for
- stsv (sorted tsv) to matrix
- matrix to phylip
Make example data:
# use bash -c '' trick to set a stable random seed for this example
bash -c '
RANDOM=42;
for i in {1..4}; do
for j in `seq $(($i+1)) 4`; do
if [ $i == $j ]; then
rand=0;
else
rand=$RANDOM;
fi;
echo -e "$i\t$j\t$rand";
done;
done' > distances.tsv
cat distances.tsv
1 2 17766
1 3 11151
1 4 23481
2 3 32503
2 4 7018
3 4 25817Convert to phylip from tsv format.
In this example since distances back and forth between samples are not defined,
there are stderr messages showing what was corrected.
If distances are defined and not equal, they will be averaged.
You can make the distances one-sided with --no-symmetric.
perl scripts/dists2.pl --outformat phylip < distances.tsv | column -t
dists2.pl: Setting 2 1 to 17766
dists2.pl: Setting 3 1 to 11151
dists2.pl: Setting 4 1 to 23481
dists2.pl: Setting 3 2 to 32503
dists2.pl: Setting 4 2 to 7018
dists2.pl: Setting 4 3 to 25817
4
1 0 17766 11151 23481
2 17766 0 32503 7018
3 11151 32503 0 25817
4 23481 7018 25817 0perl scripts/dists2.pl --outformat phylip < distances.tsv | \
perl scripts/diststree.pl
(2:3751.75,(3:9843.75,1:1307.25):15807.25,4:3266.25);Bootstraps are a test of how different kinds of perturbations or randomness will affect your tree. So for this example, I will make some randomness in the input.
mkdir bootstraps
for i in {1..100}; do
cat distances.tsv | \
perl -lane '
# give distances ±50
$rand = int(rand(100));
$rand = $rand - 50;
$F[2] += $rand;
# Print the new value to stdout
print join("\t", @F);
' > bootstraps/dist.$i.tsv;
# Transform these distances to phylip and then into a tree.
# The trees are being printed to stdout, but
# stdout will be printed to a file at the end of the loop.
perl scripts/dists2.pl --outformat phylip < bootstraps/dist.$i.tsv | \
perl scripts/diststree.pl
done > bootstraps.dnd
# => bootstraps.dnd should have 100 trees in it now
# Get rid of the folder with distances in it, now that we have BS trees
rm -rf bootstraps
head -n 3 bootstraps.dnd
(2:3739.5,(3:9834,1:1271):15834,4:3283.5);
(2:3754.5,(3:9849,1:1338):15753.5,4:3279.5);
(2:3702.75,(3:9850.75,1:1329.25):15806.75,4:3300.25);Run gotree to add supports
perl scripts/dists2.pl --outformat phylip < distances.tsv | \
perl scripts/diststree.pl | \
gotree compute support classical --bootstrap bootstraps.dnd > withbs.dnd
Classical Support
Start : 26 Jun 24 14:55 EDT
Input tree : stdin
Boot trees : bootstraps.dnd
Output tree : stdout
CPUs : 1
dists2.pl: Setting 2 1 to 17766
dists2.pl: Setting 3 1 to 11151
dists2.pl: Setting 4 1 to 23481
dists2.pl: Setting 3 2 to 32503
dists2.pl: Setting 4 2 to 7018
dists2.pl: Setting 4 3 to 25817
End : 26 Jun 24 14:55 EDTDraw the tree for fun
cat withbs.dnd
(2:3751.75,(3:9843.75,1:1307.25)1:15807.25,4:3266.25);
cat withbs.dnd | gotree draw text
+---------------------------- 2
|
| +--------------------------------------------------------------------------- 3
|--------------------------------------------------------------------------------------------------------------------------|
| +--------- 1
|
+------------------------ 4