| Name | starfile JSON |
| Version |
0.5.10
JSON |
| download |
| home_page | None |
| Summary | STAR file I/O in Python |
| upload_time | 2024-11-18 22:46:03 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.8 |
| license | BSD-3-Clause |
| keywords |
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
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| coveralls test coverage |
No coveralls.
|
# starfile
[](https://github.com/teamtomo/starfile/raw/main/LICENSE)
[](https://pypi.org/project/starfile)
[](https://python.org)
[](https://github.com/teamtomo/starfile/actions/workflows/ci.yml)
[](https://codecov.io/gh/teamtomo/starfile)
*starfile* is a package for reading and writing
[STAR files](https://en.wikipedia.org/wiki/Self-defining_Text_Archive_and_Retrieval) in Python.
<p align="center" width="100%">
<img width="70%" src="https://user-images.githubusercontent.com/7307488/204108873-c2175153-fb5b-4b22-892a-0a1274616057.png">
</p>
*starfile* can be used interactively to inspect/explore files or in
scripts and larger software packages to provide basic STAR file I/O functions.
Data is exposed as simple python dictionaries or
[pandas dataframes](https://pandas.pydata.org/docs/user_guide/dsintro.html#dataframe).
This package was designed principally for compatibility with files generated by
[RELION](https://www3.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page).
For more information on working with dataframes, please see the
[pandas docs](https://pandas.pydata.org/docs/user_guide/10min.html).
For *starfile* specific documentation, see [teamtomo.org/starfile](https://teamtomo.org/starfile)
---
# Quickstart
For the following file `particles.star` with a single data block
```txt
data_particles
loop_
_rlnCoordinateX #1
_rlnCoordinateY #2
_rlnCoordinateZ #3
_rlnAngleRot #4
_rlnAngleTilt #5
_rlnAnglePsi #6
_rlnMicrographName #7
91.798700 83.622600 203.341030 -51.740000 173.930000 32.971000 01_10.00Apx.mrc
97.635800 80.437000 203.136160 141.500000 171.760000 -134.680000 01_10.00Apx.mrc
92.415200 88.842700 210.663900 -78.750000 173.930000 87.263200 01_10.00Apx.mrc
94.607830 93.135410 205.425960 -85.215000 167.170000 85.632200 01_10.00Apx.mrc
86.187800 80.125400 204.558750 14.910000 163.260000 -16.030000 01_10.00Apx.mrc
91.824240 76.738300 203.794280 39.740000 168.410000 -57.250000 01_10.00Apx.mrc
98.253300 73.530100 203.856030 73.950000 166.380000 -84.640000 01_10.00Apx.mrc
101.303500 80.290800 194.790400 -178.878000 166.090000 73.181000 01_10.00Apx.mrc
```
Read the file
```python
import starfile
df = starfile.read('particles.star')
```
Interact with the data
```python
df['rlnCoordinateX'] += 10
df.head()
```
```txt
rlnCoordinateX rlnCoordinateY rlnCoordinateZ rlnAngleRot rlnAngleTilt rlnAnglePsi rlnMicrographName
0 101.79870 83.62260 203.34103 -51.740 173.93 32.9710 01_10.00Apx.mrc
1 107.63580 80.43700 203.13616 141.500 171.76 -134.6800 01_10.00Apx.mrc
2 102.41520 88.84270 210.66390 -78.750 173.93 87.2632 01_10.00Apx.mrc
3 104.60783 93.13541 205.42596 -85.215 167.17 85.6322 01_10.00Apx.mrc
4 96.18780 80.12540 204.55875 14.910 163.26 -16.0300 01_10.00Apx.mrc
```
Save the (modified) data to file
```python
starfile.write(df, 'modified_particles.star')
```
For more advanced usage please check out the examples.
---
# Installation
```shell
pip install starfile
```
Raw data
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