https://github.com/regmibijay/opencarp-analyzer
Reads Trace Files created by OpenCARP Models and exports data for easy plotting with inbuilt plotter script.
https://github.com/regmibijay/opencarp-analyzer
bioinformatics data-analysis opencarp
Last synced: 5 months ago
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Reads Trace Files created by OpenCARP Models and exports data for easy plotting with inbuilt plotter script.
- Host: GitHub
- URL: https://github.com/regmibijay/opencarp-analyzer
- Owner: regmibijay
- Created: 2021-04-04T14:45:26.000Z (about 5 years ago)
- Default Branch: main
- Last Pushed: 2021-04-11T07:42:10.000Z (about 5 years ago)
- Last Synced: 2025-11-27T13:57:14.113Z (7 months ago)
- Topics: bioinformatics, data-analysis, opencarp
- Language: Python
- Homepage:
- Size: 35.2 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# OpenCARP-Analyzer
creates a list of csv-formatted files for each ion channel and current with inbuilt `opencarp-analyzer` command and then plots them as line graph with `opencarp-plotter` command.
## OpenCARP-Analyzer
Data generation module
```
_____________________________________________________
OpenCARP Analyzer
Extracts data and multiple txt files from Trace data created by openCARP at once.
_____________________________________________________
usage: analyzer.py [-h] [-c COLUMNS [COLUMNS ...]] [-t TRACE] [-i IION [IION ...]] [-s [SUFFIX]] [-v [VERSION]]
optional arguments:
-h, --help show this help message and exit
-c COLUMNS [COLUMNS ...], --columns COLUMNS [COLUMNS ...]
Name of files that contain header data
-t TRACE, --trace TRACE
Trace data file, e.g. Trace_0.dat
-i IION [IION ...], --iion IION [IION ...]
Ion you want to visualize, e.g. -i i_Ks
-s [SUFFIX], --suffix [SUFFIX]
Suffix to be added behind every exported file name.
-v [VERSION], --version [VERSION]
Displays current version of the script
```
## OpenCARP-Plotter
Data visualization module
```
_____________________________________________________
OpenCARP Plotter
Plots multiple txt files created by opencarp at once.
_____________________________________________________
usage: plotter.py [-h] [-f FILES [FILES ...]] [-o OUT] [-i IGNORE [IGNORE ...]] [-t TITLE [TITLE ...]]
[-l LEGEND [LEGEND ...]] [-xlabel XLABEL [XLABEL ...]] [-ylabel YLABEL [YLABEL ...]]
[-xlim XLIM [XLIM ...]] [-ylim YLIM [YLIM ...]] [-custom CUSTOM [CUSTOM ...]] [-v [VERSION]]
optional arguments:
-h, --help show this help message and exit
-f FILES [FILES ...], --files FILES [FILES ...]
Files to Plot
-o OUT, --out OUT Output image name
-i IGNORE [IGNORE ...], --ignore IGNORE [IGNORE ...]
Ignores a file name if this text exists in file
-t TITLE [TITLE ...], --title TITLE [TITLE ...]
Title of plot
-l LEGEND [LEGEND ...], --legend LEGEND [LEGEND ...]
Legend location in plot. Options: BEST,UPPER RIGHT,UPPER LEFT,LOWER LEFT,LOWER
RIGHT,RIGHT,CENTER LEFT,CENTER RIGHT,LOWER CENTER,UPPER CENTER,CENTER
-xlabel XLABEL [XLABEL ...]
Label for x-Axis in plot
-ylabel YLABEL [YLABEL ...]
Label for y-Axis in plot
-xlim XLIM [XLIM ...]
Limit for x-Axis, start and end separated by space.
-ylim YLIM [YLIM ...]
Limit for y-Axis, start and end separated by space.
-custom CUSTOM [CUSTOM ...]
Kwargs for matplotlib
-v [VERSION], --version [VERSION]
Displays current version of the scripts
```
## Installation
Install current version of this toolkit using
`pip install opencarp-analyzer`
or using `pip install git+https://github.com/regmibijay/opencarp-analyzer`
## Usage
After installation, make sure your pip installation site is in your PATH. If so, you will be able to use `opencarp-analyzer` and `opencarp-plotter` from CLI.
## Examples
`opencarp-analyzer -c header1.txt header2.txt -t Trace_0.dat -i i_Ks V i_NCX `
will read `header1.txt` and `header2.txt` and combine column names so content of `header1.txt` is before `header2.txt`. After that it reads `Trace_0.dat` and creates a dataframe with given column names. Then the given `i_Ks`, `V` and `i_NCX` files are generated in `.txt` format with respective values from `Trace_0.dat`.
`opencarp-plotter -f data/i_*.txt data_2/*.txt -i MurineMouse header -t Comparision of voltages in mV -legend upper right`
will read `data` folder and extract all the files containing `i_` in the name and `.txt` extension. Then it will search for `*.txt` files in `data2` folder and make a list of all files, from which all files containing either `MurineMouse` or `header` in filename are omitted. Now we create a plot with title of `Comparision of voltages in mV` and legends in upper right corner.
## To Do
Current features being considered:
`color-palettes` to specify custom colors for each line.
If you want certain features, feel free to open a [feature request](https://github.com/regmibijay/opencarp-analyzer/issues).