Sampler takes a multi-FASTA (not an alignment!) or an EMBOSS-formatted distance matrix and samples a requested number of sequences from it, trying to be as comprehensive as possible. If a FASTA file is supplied and the distance matrix is not, the distances are calculated by Scoredist metric.
Returns a reduced distance matrix and, if possible, a reduced FASTA file.
git clone https://github.com/SynedraAcus/sampler
cd sampler
To reduce a dataset, call sampler.py. Either -f, -d or both should
always be supplied. Common uses:
Sample half of the sequences from aminoacid FASTA Builds distance matrix internally
./sampler.py -f sequences.fasta -p -n 0.5
Sample exactly ten sequences from the same file
./sampler.py -f sequences.fasta -p -n 10
Sample half of the sequences, using the supplied matrix FASTA file is used only for creating output files and can be omitted
./sampler.py -f sequences.fasta -d matrix.txt -p -n 0.5
Get only IDs of the selected sequences
./sampler.py -f sequences.fasta -d matrix.txt -p -i -n 0.5
If FASTA is not supplied, FASTA output cannot be produced and -i is added implicitly
./sampler.py -d matrix.txt -n 0.5
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Python 3
-
Biopython
-
numpy (tested on 1.8.2 but should probably work on older versions)
-
EMBOSS 6.6.0.0
Make sure EMBOSS needle is available in your $PATH. If it is not
possible (but you do have EMBOSS installed), add EMBOSS/bin directory
path to the NEEDLE_CALL variable in reductor.py
Sampler uses needle for pairwise alignment, a crucial step in the
distance matrix construction. As such, without needle it can only work
with supplied distance matrices.
-f Multi-FASTA file
-d PHYLIP-formatted square distance matrix in lower triangular format
-n Number (int) or proportion (float) of sequences to sample
-p FASTA contains aminoacid sequences. Defaults to False
-i Print only IDs of selected sequences. Defaults to False
-h Print option list and quit
The sampler script is just a wrapper around the reductor.py library,
which can be used directly in your Python3 projects. Two classes can be
imported from this library: DistanceMatrix, which is a numpy-based
distance matrix implementation supporting the sampling procedure, and a
DistanceMatrixFactory to create or read matrices. The description of
the API is available from classes' and methods' docstrings.
This software is distributed under the terms of CC-BY 4.0 license. The complete text of the license is available at:
https://creativecommons.org/licenses/by/4.0/legalcode
When used in a scientific publication, please cite this paper:
A.A. Morozov, Y.P. Galachyants 2017 "Distant joining: a sequence sampling method for the complex evolutionary histories".