# pySLiM
SLiM can now read, and write tree sequences, which store genealogical data of populations.
SLiM can use a tree sequence produced by the coalescent simulator `msprime` to initialize
a simulation, but to do so we need to add the relevant metadata. SLiM can also write out
history as a tree sequence, and in so doing it records extra information in metadata.
This package makes it easy to add the relevant metadata to a tree sequence so that SLiM
can use it, and to read the metadata in a SLiM-produced tree sequence.
## Installation
To install `pyslim`, do
```
git clone https://github.com/tskit-dev/pyslim.git
cd pyslim
python setup.py install --user
```
You'll also need an up-to-date [msprime](https://github.com/tskit-dev/msprime) and [SLiM](https://messerlab.org/slim/), of course.
To run the tests to make sure everything is working, do:
```
cd tests/examples
for x in *.slim; do slim $x; done
cd -
python -m nose tests
```
*Note:* if you use `python3` you may need to replace `python` with `python3` above.
## Quickstart: coalescent simulation for SLiM
The `pyslim.annotate()` command will add default information to a tree sequence, allowing
it to be read in by SLiM. This will simulate a tree sequence with msprime, add SLiM information,
and write it out to a `.trees` file:
```
import msprime
import pyslim
# simulate a tree sequence of 12 nodes
ts = msprime.simulate(12, mutation_rate=1.0, recombination_rate=1.0)
new_ts = pyslim.annotate_defaults(ts)
new_ts.dump("slim_ts.trees")
```
## Quickstart: reading SLiM metadata
To retrieve the extra information that SLiM stores in a tree sequence, use the `extract_X_metadata()`
functions. For instance, to see the age of each Individual produced by annotation
in the previous example:
```
for ind in extract_mutation_metadata(new_ts.tables):
print(ind.age)
```
## Important notes:
1. `tskit` "nodes" correspond to SLiM "genomes". Individuals are diploid, so each individual has two nodes.
2. The currently alive individuals will be those in the Individual table; all other nodes will *not*
have a corresponding individual.
3. The "remembered nodes" will be the *first* nodes.
SLiM can now read, and write tree sequences, which store genealogical data of populations.
SLiM can use a tree sequence produced by the coalescent simulator `msprime` to initialize
a simulation, but to do so we need to add the relevant metadata. SLiM can also write out
history as a tree sequence, and in so doing it records extra information in metadata.
This package makes it easy to add the relevant metadata to a tree sequence so that SLiM
can use it, and to read the metadata in a SLiM-produced tree sequence.
## Installation
To install `pyslim`, do
```
git clone https://github.com/tskit-dev/pyslim.git
cd pyslim
python setup.py install --user
```
You'll also need an up-to-date [msprime](https://github.com/tskit-dev/msprime) and [SLiM](https://messerlab.org/slim/), of course.
To run the tests to make sure everything is working, do:
```
cd tests/examples
for x in *.slim; do slim $x; done
cd -
python -m nose tests
```
*Note:* if you use `python3` you may need to replace `python` with `python3` above.
## Quickstart: coalescent simulation for SLiM
The `pyslim.annotate()` command will add default information to a tree sequence, allowing
it to be read in by SLiM. This will simulate a tree sequence with msprime, add SLiM information,
and write it out to a `.trees` file:
```
import msprime
import pyslim
# simulate a tree sequence of 12 nodes
ts = msprime.simulate(12, mutation_rate=1.0, recombination_rate=1.0)
new_ts = pyslim.annotate_defaults(ts)
new_ts.dump("slim_ts.trees")
```
## Quickstart: reading SLiM metadata
To retrieve the extra information that SLiM stores in a tree sequence, use the `extract_X_metadata()`
functions. For instance, to see the age of each Individual produced by annotation
in the previous example:
```
for ind in extract_mutation_metadata(new_ts.tables):
print(ind.age)
```
## Important notes:
1. `tskit` "nodes" correspond to SLiM "genomes". Individuals are diploid, so each individual has two nodes.
2. The currently alive individuals will be those in the Individual table; all other nodes will *not*
have a corresponding individual.
3. The "remembered nodes" will be the *first* nodes.
2 maintainers
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distributions
No source distribution files available for this release.See tutorial on generating distribution archives.
Built Distribution
Filter files by name, interpreter, ABI, and platform.
If you're not sure about the file name format, learn more about wheel file names.
Copy a direct link to the current filters
pyslim-0.0.51-py3-none-any.whl
(24.0 kB
view details)
File details
Details for the file pyslim-0.0.51-py3-none-any.whl.
File metadata
- Download URL: pyslim-0.0.51-py3-none-any.whl
- Upload date:
- Size: 24.0 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
0fa790e435822971882a4568456284c4397dd8ef94db8269d1ed5ce593714f9a
|
|
| MD5 |
22b69d8bf69365293ba33d358ee76ec3
|
|
| BLAKE2b-256 |
408f90f5451f185d7bcf59cb50b5f76090f726888a5c4b39b8a87934780cf7dd
|
