simulatesv

Simulate Structural Variations and SNPs for artificial DNA templates. The DNA templates are generated simply with a pseudo-random number generator, and is not guided by biological significance. The tool is provided with the intention of creating a validation set of variants to test current structural variation detection tools.

Installation

The recommended method is to install via pip or git clone. You can also get the source distribution from pypi. pip will install all the necessary dependencies for you.

$ pip install simulatesv 

or

$ git clone git@github.com:mlliou112/simulatesv.git
$ python setup.py install

Usage

This script runs with either Python 2 or 3, and requires the Python package numpy to run.

If you install via pip, the script will be available to run as simulatesv.py, or python simulatesv.py if you installed via git clone.

Basic

$ python simulatesv.py

This will run the program with all defaults, making one 50 kbp reference genome and three simulated genomes in the current working directory. (total 7 files)

.
├── reference.fna  # randomly generated dna template on which mutations are made
├── sim_0.fna      # first simulated genome based off reference with SNPs and SVs
├── sim_1.fna      # 2nd ...
├── sim_2.fna      # 3rd ...
├── changes_0.txt  # log of what changes were made to the reference genome to create the first simulated genome
├── changes_1.txt  # 2nd change log ...
└── changes_2.txt  # 3rd change log ...

You may add a seed number to make the simulation reproducible. We can also specify the number of simulated genomes to make and the length of the generated reference.

$ python simulatesv.py --seed 10 --number 5 --length 60000

If you have your own genome template that you would like to simulate variants from, you can specify the FASTA file with the -t FILE option. You can also modify the frequency of each variant as well as their size.

See the Command Reference below for more options.

$ python simulatesv.py -t reference.fna -n 20 --snp-error-rate .005 --largest-insertion-size 200

Changes

The changes file logs what changes are made to the reference sequence. A "." marks that column as a null dna sequence. The file is sorted by ref_idx.

Notes

• If you are simulating a small DNA template (< 500), make sure that SV option sizes are less than the total size of your genomes, otherwise you may run into unknown issues.

• Mutation rates for SVs and SNPs are approximate. A binomial model is used to determine the actual number of mutations based off of the given error rate.

• There is a subtle difference for the meanings of the idx columns between indels and translocations for the changes file. For translocations, the idx will track the dna sequence, and will not track the null sequences of where the sequence was deleted or inserted. That is, if you think of a translocation as one deletion and one insertion, there will be two columns tracking the ref_idx of the insertion and two alt_idx for the deletion.

Command Reference

usage: simulate.py [-h] [-n N] [-s SEED] [-l N | -t FILE] [-b BASE] [-o FILE]
                   [-c BASE] [-se ERR] [-ie ERR] [-de ERR] [-lis N] [-lds N]
                   [-sis N] [-sds N] [-te ERR] [-lts N] [-sts N] [-ce ERR]
                   [-lcn N] [-scn N] [-lcs N] [-scs N]

Simulate DNA template sequences with known SNPs and structural variations.

optional arguments:
  -h, --help            show this help message and exit
  -n N, --number N      Number of simulated genome sequences to generate.
                        (default=3)
  -s SEED, --seed SEED  Pseudorandom number generator seed. Set number to
                        reproduce genomes and changes.
  -l N, --length N      Total length of reference genome sequence.
                        (default=50000)
  -t FILE, --template FILE
                        Template to use as a base for generating SNP/SV in
                        Fasta format.

Output File Options:
  -b BASE, --basename BASE
                        Basename of the simulated fake sequences.
                        (default=sim_)
  -o FILE, --output FILE
                        Reference file for the mutated template
                        (default=reference.fna)
  -c BASE, --changes BASE
                        Basename of the changes files (default=changes_)

SNP Options:
  -se ERR, --snp-error-rate ERR
                        Error rate for SNPs (default=.001)

Indel Options:
  -ie ERR, --insertion-error-rate ERR
                        Error rate for insertions (default=.0001)
  -de ERR, --deletion-error-rate ERR
                        Error rate for deletions (default=.0001)
  -lis N, --largest-insertion-size N
                        Largest insertion size (default=500)
  -lds N, --largest-deletion-size N
                        Largest deletion size (default=500)
  -sis N, --smallest-insertion-size N
                        Smallest insertion size (default=1)
  -sds N, --smallest-deletion-size N
                        Smallest deletion size(default=1)

Trans Options:
  -te ERR, --trans-error-rate ERR
                        Error rate for translocations (default=.0001)
  -lts N, --largest-trans-size N
                        Largest translocation size (default=500)
  -sts N, --smallest-trans-size N
                        Smallest translocation size (default=10)

CNV Options:
  -ce ERR, --cnv-error-rate ERR
                        Error rate for CNVs (default=.0001)
  -lcn N, --largest-cnv-number N
                        Maximum number of times the CNV can repeat
  -scn N, --smallest-cnv-number N
                        Minimum number of times the CNV will repeat
  -lcs N, --largest-cnv-size N
                        Largest size for CNVs (default=300)
  -scs N, --smallest-cnv-size N
                        Smallest size for CNVs (default=2)

Contributing

Bug reports, feature requests, and pull requests are encouraged!

License

MIT