Metadata-Version: 2.1
Name: KOnezumiAID
Version: 0.1.1
Summary: Project description
License: MIT
Author: Taki Taito
Author-email: s2110307@u.tsukuba.ac.jp
Requires-Python: >=3.9,<4.0
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: MacOS
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Dist: numpy (==1.26.0)
Requires-Dist: pandas (==2.2.2)
Requires-Dist: primer3-py (>=2.0.1,<3.0.0)
Description-Content-Type: text/markdown

# Hello KOnezumi-AID

## Input data set

### genomic sequence
`mm39.fa.gz` from [UCSC](
https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/
)


### Locus information
`refFlat.text` from [UCSC](
https://hgdownload.soe.ucsc.edu/goldenPath/mm39/database/
)

### Download scripts (bash)

```bash
mkdir -p data
wget -O - https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/mm39.fa.gz |
    gzip -dc > data/mm39.fa
wget -O - https://hgdownload.soe.ucsc.edu/goldenPath/mm39/database/refFlat.txt.gz |
    gzip -dc > data/refFlat.txt
```


#### Use as pandas.DataFrame in this code
DataFrame refFlat has 11 columns.
- string  geneName;           "Name of gene as it appears in Genome Browser." 
- string  name;               "Name of gene" 
- string  chrom;              "Chromosome name" 
- char[1] strand;             "+ or - for strand" 
- uint    txStart;            "Transcription start position" 
- uint    txEnd;              "Transcription end position" 
- uint    cdsStart;           "Coding region start" 
- uint    cdsEnd;             "Coding region end" 
- uint    exonCount;          "Number of exons" 
- uint[exonCount] exonStarts; "Exon start positions" 
- uint[exonCount] exonEnds;   "Exon end positions" 

