xiangpin/bioftparse

:hammer: tookits to parse multiple format files in bioinformatics

BioFtParse

This package will save some scripts to parse some common bioinformatic format file. Now, it only contain parse_genbank.py to parse the genebank file, and generate fasta file contained sequences, CDS annotation table, and Seq annotation table.

Install

It depends on python3. So your computer should have been installed python3 before install it.

git clone https://github.com/xiangpin/BioFtParse.git
python setup.py install
# or sudo python setup.py install

Usage

There are some examples in examples. Or you can view the help information with the following code.

parse_genbank.py -h

## usage: parse_genbank.py [-h] [-s seqfasta] [-t seqannot] [-c cdsannot] genbank
## 
## Description:
## This Script was designed to extract sequences, the descriptions of seqences
## and the annotation of CDS from GenBank files.
## Developer: Shuangbin Xu.
## Email: [email protected]
## 
## positional arguments:
##   genbank      input file, the GenBank format file
## 
## optional arguments:
##   -h, --help   show this help message and exit
##   -s seqfasta  the output of sequences, default is GenBankSeq.fasta
##   -t seqannot  the output of sequences annotation, default is GenBankSeq.annot
##   -c cdsannot  the output of CDS annotation, default is GenBankCDS.annot