polish_genbank

1 Introduction

see https://github.com/linzhi2013/polish_genbank.

This package is to check for the internal stop codon in Genbank or FASTA file (CDS), then substitute the internal stop codon with NNN.

2 Installation

pip3 install polish_genbank

There will be a command polish_genbank created under the same directory as your pip3 command.

3 Usage

run polish_genbank

usage: polish_genbank.py [-h] --in <file> [--format {gb,fa}] [--table <int>]
                         [--ntNs <str>] [--aaNs <str>] --out <file>

Check for the internal stop codon, then substitute the internal stop codon
with NNN. By mengguanliang [] genomics.cn, where [] == @. See
https://github.com/linzhi2013/polish_genbank

optional arguments:
  -h, --help        show this help message and exit
  --in <file>       input genbank file or CDS file (fasta format)
  --format {gb,fa}  the input file format. For fasta file, all sequences are
                    assumed to be forward strand, coding from +1 position [gb]
  --table <int>     The genetic code table used for translation, for fasta
                    input only [2]
  --ntNs <str>      the chars used for substituting an internal stop codon in
                    CDS sequence. [NNN]
  --aaNs <str>      the chars used for substituting an internal stop codon in
                    protein sequence. [X]
  --out <file>      output filename

4 Used in scripts

In [1]: from polish_genbank import polish_gb, polish_fasta

In [2]: polish_gb?
Signature: polish_gb(ingb=None, NewInternalStopCodonNT='NNN', NewInternalStopCodonAA='X', logger=None)
Docstring:
Replace the internal stop codon with NNNs on Genbank nt sequence,
and replace the '*' in 'translation' tag (protein sequence) with 'X'

Return:
    An generator.

Usage:

>>> records = polish_gb(ingb='in.gb', NewInternalStopCodonNT='NNN',
        NewInternalStopCodonAA='X')
>>> for rec in records:
>>>     print(rec.id, rec.seq)


In [3]: polish_fasta?
Signature: polish_fasta(infasta=None, NewInternalStopCodonNT='NNN', table=2, logger=None)
Docstring:
Replace the internal stop codon with NNNs.

The infasta file is assumed to be CDS sequences, and coding from +1
position.

Return:
    An generator.

Usage:

>>> records = polish_fasta(infasta='myfile', NewInternalStopCodonNT='NNN', table=2)
>>> for rec in records:
>>>     print(rec.id, rec.seq)

5 Citation

Currently I have no plan to publish polish_genbank.

However, since polish_genbank makes use of Biopython, you should also cite it if you use breakSeqInNs_then_translate in your work:

Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski, Michiel J. L. de Hoon: “Biopython: freely available Python tools for computational molecular biology and bioinformatics”. Bioinformatics 25 (11), 1422–1423 (2009). https://doi.org/10.1093/bioinformatics/btp163

Please go to http://www.biopython.org/ for more details.