featurExtract 0.2.6.0
Extract genome ferature sequence for biologists
License: MIT
Requires Python: >=3.7.6
Keywords: genome feature,extract

# Overview

The featurExtract is a python package for genome feature extraction in bioinformatics.  
The package contains two useful executable command programs. The first executable program 
is featurExtract including ten subroutines termed create, gene, promoter, UTR, uORF,  CDS,
dORF, exon, intron, intergenic. The second executable program is create that is used for 
creating database. The promoter subroutine is used for extracting promoter sequence. The 
uORF subroutine is used for extracting upstream open reading frames sequence. The UTR 
subroutine is used for extracting untranslated region sequence. The CDS subroutine is used 
for extracting coding sequence. The intergenic subroutine is used for extracting intergenic 
sequence between two genes. The second executable program is genBankExtract including  
four subroutines termed gene, CDS, rRNA, tRNA.


## Brief introduction of featurExtract package

### Install
Two way offer to install featurExtract module.

#### install command line

```bash
pip install featurExtract
# other
git clone https://github.com/SitaoZ/featurExtract.git
cd featurExtract
python setup.py install
```

#### Requirements

python >= 3.7.6 [python](https://www.python.org/)  
pandas >= 1.2.4 [pandas](https://pandas.pydata.org/docs/)  
gffutils >= 0.10.1 [gffutils](https://pythonhosted.org/gffutils/)  
setuptools >= 49.2.0 [setuptools](https://pypi.org/project/setuptools/)  
biopython >= 1.78 [biopython](https://biopython.org/wiki/Documentation/)  

### Usage
featurExtract is designed for GFF and GTF file  
and GenBankExtract is suited for GenBank file. 

#### featurExtract

```bash
# gff or gtf database 
which featurExtract
featurExtract -h 
featurExtract create -h 
featurExtract promoter -h 
featurExtract UTR -h 
featurExtract uORF -h 
featurExtract CDS -h 
featurExtract dORF -h
featurExtract exon -h
featurExtract intron -h
featurExtract intergenic -h
```

#### genBankExtract

```bash 
# GenBank database
which genBankExtract
genBankExtract -h
genBankExtract gene -h
genBankExtract CDS  -h
genBankExtract rRNA -h
genBankExtract tRNA -h
```
### Examples

#### featurExtract

```bash
# step 1 create database
featurExtract create -f GFF -g ath.gff3 -o ath
# step 2 command
# promoter whole genome
featurExtract promoter -d ath.GFF -f ath.fa -l 200 -u 100 -o promoter.csv --output_format fasta
# promoter one gene to stdout 
featurExtract promoter -d ath.GFF -f ath.fa -l 200 -u 100 -g AT1G01010 -p --output_format fasta
featurExtract UTR -d ath.GFF -f ath.fa -o UTR.csv -s GFF
featurExtract uORF -d ath.GFF -f ath.fa -o uORF.csv -s GFF
featurExtract CDS -d ath.GFF -f ath.fa -o CDS.csv -s GFF
featurExtract mRNA -d ath.GFF -f ath.fa -o mRNA.fasta -s GFF --output_format fasta
featurExtract exon -d ath.GFF -f ath.fa -t AT1G01010.1 -p -s GFF
featurExtract intron -d ath.GFF -f ath.fa -t AT1G01010.1 -p -s GFF
```
    
#### genBankExtract

```bash 
# GenBank step 3
genBankExtract gene -g NC_000932.gb -f dna -p  
genBankExtract CDS  -g NC_000932.gb -f dna -p 
genBankExtract rRNA -g NC_000932.gb -f dna -p
genBankExtract tRNA -g NC_000932.gb -f dna -p
```