# 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
```
Raw data
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"description": "# Overview\n\nThe featurExtract is a python package for genome feature extraction in bioinformatics. \nThe package contains two useful executable command programs. The first executable program \nis featurExtract including ten subroutines termed create, gene, promoter, UTR, uORF, CDS,\ndORF, exon, intron, intergenic. The second executable program is create that is used for \ncreating database. The promoter subroutine is used for extracting promoter sequence. The \nuORF subroutine is used for extracting upstream open reading frames sequence. The UTR \nsubroutine is used for extracting untranslated region sequence. The CDS subroutine is used \nfor extracting coding sequence. The intergenic subroutine is used for extracting intergenic \nsequence between two genes. The second executable program is genBankExtract including \nfour subroutines termed gene, CDS, rRNA, tRNA.\n\n\n## Brief introduction of featurExtract package\n\n### Install\nTwo way offer to install featurExtract module.\n\n#### install command line\n\n```bash\npip install featurExtract\n# other\ngit clone https://github.com/SitaoZ/featurExtract.git\ncd featurExtract\npython setup.py install\n```\n\n#### Requirements\n\npython >= 3.7.6 [python](https://www.python.org/) \npandas >= 1.2.4 [pandas](https://pandas.pydata.org/docs/) \ngffutils >= 0.10.1 [gffutils](https://pythonhosted.org/gffutils/) \nsetuptools >= 49.2.0 [setuptools](https://pypi.org/project/setuptools/) \nbiopython >= 1.78 [biopython](https://biopython.org/wiki/Documentation/) \n\n### Usage\nfeaturExtract is designed for GFF and GTF file \nand GenBankExtract is suited for GenBank file. \n\n#### featurExtract\n\n```bash\n# gff or gtf database \nwhich featurExtract\nfeaturExtract -h \nfeaturExtract create -h \nfeaturExtract promoter -h \nfeaturExtract UTR -h \nfeaturExtract uORF -h \nfeaturExtract CDS -h \nfeaturExtract dORF -h\nfeaturExtract exon -h\nfeaturExtract intron -h\nfeaturExtract intergenic -h\n```\n\n#### genBankExtract\n\n```bash \n# GenBank database\nwhich genBankExtract\ngenBankExtract -h\ngenBankExtract gene -h\ngenBankExtract CDS -h\ngenBankExtract rRNA -h\ngenBankExtract tRNA -h\n```\n### Examples\n\n#### featurExtract\n\n```bash\n# step 1 create database\nfeaturExtract create -f GFF -g ath.gff3 -o ath\n# step 2 command\n# promoter whole genome\nfeaturExtract promoter -d ath.GFF -f ath.fa -l 200 -u 100 -o promoter.csv --output_format fasta\n# promoter one gene to stdout \nfeaturExtract promoter -d ath.GFF -f ath.fa -l 200 -u 100 -g AT1G01010 -p --output_format fasta\nfeaturExtract UTR -d ath.GFF -f ath.fa -o UTR.csv -s GFF\nfeaturExtract uORF -d ath.GFF -f ath.fa -o uORF.csv -s GFF\nfeaturExtract CDS -d ath.GFF -f ath.fa -o CDS.csv -s GFF\nfeaturExtract mRNA -d ath.GFF -f ath.fa -o mRNA.fasta -s GFF --output_format fasta\nfeaturExtract exon -d ath.GFF -f ath.fa -t AT1G01010.1 -p -s GFF\nfeaturExtract intron -d ath.GFF -f ath.fa -t AT1G01010.1 -p -s GFF\n```\n \n#### genBankExtract\n\n```bash \n# GenBank step 3\ngenBankExtract gene -g NC_000932.gb -f dna -p \ngenBankExtract CDS -g NC_000932.gb -f dna -p \ngenBankExtract rRNA -g NC_000932.gb -f dna -p\ngenBankExtract tRNA -g NC_000932.gb -f dna -p\n```\n \n\n\n",
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