jeddinformatics

Release 0.6.1

Convert bioinformatics data to plots

Homepage PyPI Python

Keywords
bioinformatics, plotly
License
Unlicense
Install
pip install jeddinformatics==0.6.1

Documentation

Jeddinformatics

Initial setup

pip install -r requirements.txt

This will install the required packages

Running on errything

python3 main.py <your data folder>

Config files

{
    "$schema": "https://raw.githubusercontent.com/wolffshots/jeddinformatics/main/src/jeddinformatics/schema.json",
    "mappings": {
        "normal": "NC",
        "Normal": "NC",
        "OV": "OV",
        "UCEC": "UCEC",
        "Ovarian Cancer": "OV",
        "Uterine Cancer": "UCEC",
        "Some title": "Translated title",
        "log2(TPM)": "log<sub>2</sub>(TPM)"
    },
    "colors": {
        "NC": "blue",
        "OV": "green",
        "UCEC": "red",
        "box": "black",
        "plot_background_color": "lightgray",
        "paper_background_color": "white"
    },
    "precedence": ["NC", "normal", "Normal"],
    "jitter": 0.5,
    "line_width": 1.5,
    "point_size": 6,
    "plot_height": 540,
    "plot_width": 960
}

Building and distributing

rm -fr dist && python3 -m build && python3 -m twine upload --repository testpypi dist/*

Rename all to OV (Ovarian canver) and UCEC (Uterine cancer) and make "normal"/"Normal" to NC (Non-cancer)

Data should look like:

β”‚   
β”œβ”€β”€β”€Gene Expression
β”‚   └───ONCODB
β”‚       β”œβ”€β”€β”€Ovarian Cancer
β”‚       β”‚   β”œβ”€β”€β”€CAS
β”‚       β”‚   β”‚       data.txt
β”‚       β”‚   β”‚       
β”‚       β”‚   β”œβ”€β”€β”€IPO5
β”‚       β”‚   β”‚       data.txt
β”‚       β”‚   β”‚       
β”‚       β”‚   β”œβ”€β”€β”€KPNA2
β”‚       β”‚   β”‚       data.txt
β”‚       β”‚   β”‚       
β”‚       β”‚   β”œβ”€β”€β”€KPNB1
β”‚       β”‚   β”‚       data.txt
β”‚       β”‚   β”‚       
β”‚       β”‚   β”œβ”€β”€β”€RAN
β”‚       β”‚   β”‚       data.txt
β”‚       β”‚   β”‚       
β”‚       β”‚   β”œβ”€β”€β”€TNPO1
β”‚       β”‚   β”‚       data.txt
β”‚       β”‚   β”‚       
β”‚       β”‚   └───XPO1
β”‚       β”‚           data.txt
β”‚       β”‚           
β”‚       └───Uterine Cancer
β”‚           β”œβ”€β”€β”€CAS
β”‚           β”‚       data.txt
β”‚           β”‚       
β”‚           β”œβ”€β”€β”€IPO5
β”‚           β”‚       data.txt
β”‚           β”‚       
β”‚           β”œβ”€β”€β”€KPNA2
β”‚           β”‚       data.txt
β”‚           β”‚       
β”‚           β”œβ”€β”€β”€KPNB1
β”‚           β”‚       data.txt
β”‚           β”‚       
β”‚           β”œβ”€β”€β”€RAN
β”‚           β”‚       data.txt
β”‚           β”‚       
β”‚           β”œβ”€β”€β”€TNPO1
β”‚           β”‚       data.txt
β”‚           β”‚       
β”‚           └───XPO1
β”‚                   data.txt
β”‚                   
└───Protein Expression
    └───UALCAN
        β”œβ”€β”€β”€Ovarian Cancer
        β”‚   β”œβ”€β”€β”€CAS
        β”‚   β”‚       data.json
        β”‚   β”‚       
        β”‚   β”œβ”€β”€β”€IPO5
        β”‚   β”‚       data.json
        β”‚   β”‚       
        β”‚   β”œβ”€β”€β”€KPNA2
        β”‚   β”‚       data.json
        β”‚   β”‚       
        β”‚   β”œβ”€β”€β”€KPNB1
        β”‚   β”‚       data.json
        β”‚   β”‚       
        β”‚   β”œβ”€β”€β”€RAN
        β”‚   β”‚       data.json
        β”‚   β”‚       
        β”‚   β”œβ”€β”€β”€TNPO1
        β”‚   β”‚       data.json
        β”‚   β”‚       
        β”‚   └───XPO1
        β”‚           data.json
        β”‚           
        └───Uterine Cancer
            β”œβ”€β”€β”€CAS
            β”‚       data.json
            β”‚       
            β”œβ”€β”€β”€IPO5
            β”‚       data.json
            β”‚       
            β”œβ”€β”€β”€KPNA2
            β”‚       data.json
            β”‚       
            β”œβ”€β”€β”€KPNB1
            β”‚       data.json
            β”‚       
            β”œβ”€β”€β”€RAN
            β”‚       data.json
            β”‚       
            β”œβ”€β”€β”€TNPO1
            β”‚       data.json
            β”‚       
            └───XPO1
                    data.json

So general form is:

 {gene or protein expression}
  └───{source database}
       └───{type of cancer}
            └───{gene or protein name}
                 └───{data.json or data.txt}

Stats

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7
Dependent packages
0
Dependent repositories
0
Total releases
5
Latest release
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Forks
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Watchers
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Contributors
1
Repository size
45.9 KB
SourceRank
7

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Releases

0.6.1
0.5.1
0.4.2
0.4.1
0.3.0

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