pydna.editor

This module provides a class for opening a sequence using an editor that accepts a file as a command line argument.

ApE - A plasmid Editor [1] is and excellent editor for this purpose.

References

[1]

http://biologylabs.utah.edu/jorgensen/wayned/ape/

class pydna.editor.Editor(shell_command_for_editor, tmpdir=None)

Bases: object

The Editor class needs to be instantiated before use.

Parameters:

• shell_command_for_editor (str) – String containing the path to the editor

• tmpdir (str, optional) – String containing path to the temprary directory where sequence files are stored before opening.

Examples

>>> import pydna
>>> #ape = pydna.Editor("tclsh8.6 /home/bjorn/.ApE/apeextractor/ApE.vfs/lib/app-AppMain/AppMain.tcl")
>>> #ape.open("aaa") # This command opens the sequence in the ApE editor

open(seq_to_open)

Open a sequence for editing in an external (DNA) editor.

Parameters:

args (SeqRecord or Dseqrecord object) –

pydna.editor.ape(*args, **kwargs)

docstring.