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.
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
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