featurExtract 0.2.3

Extract genome ferature sequence for biologists

# Overview

The featurExtract is python package for bioinformatics. The packages contains two executable command programs. The first executable program is featurExtract including ten subroutines termed create, gene, promoter, UTR, uORF, CDS, dORF, exon, intron, intergenic. The create subroutine is used for creating database. The promoter subroutine is used for extracting promoter sequence. uORF subroutine is used for extracting upstream open reading frames sequence. UTR subroutine is used for extracting untranslated region sequence. CDS subroutine is used for extracting coding sequence.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 featurExtract create -g ath.gff3 # step 2 command featurExtract promoter -l 200 -u 100 -f ath.fa -o promoter.csv featurExtract UTR -o UTR.csv featurExtract uORF -o uORF.csv featurExtract CDS -o CDS.csv featurExtract exon -f ath.fa -t AT1G01010.1 -p featurExtract intron -f ath.fa -t AT1G01010.1 -p `

#### 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 `