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.. testsetup:: *
import gfapy
g = gfapy.Gfa()
.. _comments:
Comments
--------
GFA lines starting with a ``#`` symbol are considered comments. In Gfapy
comments are represented by instances of the class :class:`gfapy.line.Comment
<gfapy.line.comment.comment.Comment>`. They have a similar interface to other
line instances, with some differences, e.g. they do not support tags.
The comments collection
~~~~~~~~~~~~~~~~~~~~~~~
The comments of a Gfa object are accessed using the :func:`Gfa.comments
<gfapy.lines.collections.Collections.comments>` property. This is a list of
comment line instances. The single elements can be modified, but the list
itself is read-only. To remove a comment from the Gfa, you need to find the
instance in the list, and call
:func:`~gfapy.line.common.disconnection.Disconnection.disconnect` on it. To
add a comment to a :class:`~gfapy.gfa.Gfa` instance is done similarly to other
lines, by using the :func:`Gfa.add_line(line)
<gfapy.lines.creators.Creators.add_line>` method.
.. doctest::
>>> g.add_line("# this is a comment") #doctest: +ELLIPSIS
>>> [str(c) for c in g.comments]
['# this is a comment']
>>> g.comments[0].disconnect()
>>> g.comments
[]
Accessing the comment content
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
The content of the comment line, excluding the initial ``#`` and eventual
initial spacing characters, is included in the ``content`` field. The initial
spacing characters can be read/changed using the ``spacer`` field. The default
value is a single space.
.. doctest::
>>> g.add_line("# this is a comment") #doctest: +ELLIPSIS
>>> c = g.comments[-1]
>>> c.content
'this is a comment'
>>> c.spacer
' '
>>> c.spacer = '___'
>>> str(c)
'#___this is a comment'
Tags are not supported by comment lines. If the line contains tags,
these are nor parsed, but included in the ``content`` field. Trying to set
tags raises exceptions.
.. doctest::
>>> c = gfapy.Line("# this is not a tag\txx:i:1")
>>> c.content
'this is not a tag\txx:i:1'
>>> c.xx
>>> c.xx = 1
Traceback (most recent call last):
...
gfapy.error.RuntimeError: Tags of comment lines cannot be set
|
