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 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
Alternatively, clone this repository from GitHub, then run (in a python virtual environment)
If this fails on older versions of Python, try updating your
piptool first:and then rerun the
merge-gbk-recordsinstall.merge-gbk-recordsis 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-recordswill add a 20 kbp spacer of allNs and output the merged record on the terminal.You can set different lengths using
-lor--length. To use a 5 kbp spacer, use:You can select an all-frame stop codon spacer instead using
-s stopor--spacer stop:Instead of writing to stdout, you can also write to a file using
-oor--outfile:To print help about the command, just run it with
-hor--help:License
All code is available under the Apache License version 2, see the
LICENSEfile for details.