Merge multiple GenBank records using a defined spacer sequence

A small script to turn a multiple GenBank records (either in multiple files or a single multi-record file) into a single record.

Sequences are merged by concatenating them in order, and putting a spacer sequence between them. Spacer sequence length can be given in kbp. It is possible to pick an all-N spacer, or using a spacer consisting of all-frame stop codons.

Installation

pip install merge-gbk-records

Alternatively, clone this repository from GitHub, then run (in a python virtual environment)

pip install .

If this fails on older versions of Python, try updating your pip tool first:

pip install --upgrade pip

and then rerun the merge-gbk-records install.

merge-gbk-records is only developed and tested on Python releases still under active support by the Python project. At the moment, this means versions 2.7, 3.3, 3.4, 3.5 and 3.6. Specifically, no attempt at testing under Python versions older than 2.7 or 3.3 is being made.

If your system is stuck on an older version of Python, consider using a tool like Homebrew or Linuxbrew to obtain a more up-to-date version.

Usage

By default, merge-gbk-records will add a 20 kbp spacer of all Ns and output the merged record on the terminal.

merge-gbk-records first.gbk second.gbk > merged.gbk

You can set different lengths using -l or --length. To use a 5 kbp spacer, use:

merge-gbk-records --length 5 first.gbk second.gbk > merged.gbk

You can select an all-frame stop codon spacer instead using -s stop or --spacer stop:

merge-gbk-records --spacer stop first.gbk second.gbk > merged.gbk

Instead of writing to stdout, you can also write to a file using -o or --outfile:

merge-gbk-records --outfile merged.gbk first.gbk second.gbk

To print help about the command, just run it with -h or --help:

merge-gbk-records --help

License

All code is available under the Apache License version 2, see the LICENSE file for details.