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To filter the sequences by translating the protein coding genes (PCGs) with proper genetic code table, if one of the PCGs has interal stop codon, filter out this sequence. See https://github.com/linzhi2013/breakSeqInNs_then_translate

Project description

breakSeqInNs_then_translate

1 Introduction

breakSeqInNs_then_translate is a tool to filter the sequences by translating the protein coding genes (PCGs) with proper genetic code table, if one of the PCGs has interal stop codon, filter out this sequence. By Guanliang MENG, see https://github.com/linzhi2013/breakSeqInNs_then_translate.

2 Installation

pip install breakSeqInNs_then_translate

There will be a command breakSeqInNs_then_translate created under the same directory as your pip command.

3 Usage

$ breakSeqInNs_then_translate
usage: breakSeqInNs_then_translate.py [-h] [-seq <seq>] [-seqfile <file>]
                                      [-seqformat {fa,gb}] [-code <int>] [-nb]
                                      [-gb_genes <int>] [-maxStopGenes <int>]

Filter the sequences by translating the protein coding genes (PCGs) with
proper genetic code table, if one of the PCGs has interal stop codon, filter
out this sequence. Beware: if the seq has Ns, then this script will translate
the sub seqs with three frames (0, 1, 2), only when all these three kinds of
frames have interal stopCodon the seq will be treated as have InternalStop!.
By Guanliang MENG, see
https://github.com/linzhi2013/breakSeqInNs_then_translate

optional arguments:
  -h, --help           show this help message and exit
  -seq <seq>           input sequence
  -seqfile <file>      input fasta or genbank file
  -seqformat {fa,gb}   input -seqfile format [fa]
  -code <int>          genetic code table [1]
  -nb                  do not break sequence in Ns when translate [break]
  -gb_genes <int>      if a genbank record has no less than -gb_genes PCGs and
                       no more than -maxStopGenes PCGs has InternalStops, we
                       keep this record. But if a genbank record has less than
                       -gb_genes PCGs, then we will discard this record if any
                       of its PCGs has InternalStops. This is because we may
                       want to tolerate some assembly/sequencing errors. This
                       has no effect on fasta input file. [5]
  -maxStopGenes <int>  the maximum number of PCGs can have InternalStops in a
                       genbank record if do not discard it [0]

4 Author

Guanliang MENG

5 Citation

Currently I have no plan to publish breakSeqInNs_then_translate.

However, since breakSeqInNs_then_translate 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.

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