promoterExtract 0.9.5

Extract promoter sequence for biologists

# Overview

The promoterExtract is python package for bioinformatics. The packages contains two subcommands. The create subcommand is used for creating database and extract subcomand is used for extracting promoter sequence. Argument -l means the length of promoter, int type. Argument -u utr5 after TSS, int type. Argument -f reference genome fasta of a specific organism. Argument -g annotation file including GTF and GFF. Argument -o means output file path.

## Brief introduction of format package

1. Install <br>

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

2. Usage <br>

   `bash which get_promoter get_promoter -h get_promoter create -h get_promoter extract -h `

   `bash # step 1 get_promoter create -g ath.gff3 # step 2 get_promoter -l 200 -u 100 -f ath.fa -o promoter.csv `