promoterExtract 0.9.5.8

Extract promoter sequence for biologists

Overview

The promoterExtract is python package for nucleotide manipulation in bioinformatics. The package contains two subcommands including create and extract. The create subcommand is used for creating database and extract subcomand is used for extracting promoter sequence. Both two subcomand is executed through get_promoter command in command line. 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
   

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

2. Usage
   

   which get_promoter
   get_promoter -h 
   get_promoter create -h 
   get_promoter extract -h 
   

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