From c9413f13b9b1a616d954acf981354db10097db76 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Wed, 28 Aug 2019 10:22:03 +0200
Subject: [PATCH] Document parameters and return type for Sequence IO
---
modules/io/doc/io.rst | 110 ++++++++++++++++++++++++++++++++++++++++--
1 file changed, 107 insertions(+), 3 deletions(-)
diff --git a/modules/io/doc/io.rst b/modules/io/doc/io.rst
index a00d8c383..995950ed2 100644
--- a/modules/io/doc/io.rst
+++ b/modules/io/doc/io.rst
@@ -168,6 +168,12 @@ Loading sequence or alignment files
Load sequence data from disk. If format is set to 'auto', the function guesses
the filetype based on the extension of the file. Files ending in '.fasta',
'.aln' will automatically be loaded.
+
+ :param filename: The filename
+ :type filename: string
+ :param format: Name of the format
+ :type format: string
+ :rtype: :class:`~ost.seq.SequenceHandle`
For files with non-standard extensions, the format can be set explicitly
specifying the `format` parameter.
@@ -197,12 +203,24 @@ Loading sequence or alignment files
:func:`LoadSequence`. For a list of file formats supported by
:func:`LoadSequenceList` see :doc:`sequence_formats`.
+ :param filename: The filename
+ :type filename: string
+ :param format: Name of the format
+ :type format: string
+ :rtype: :class:`~ost.seq.SequenceList`
+
.. function:: LoadAlignment(filename, format='auto')
For a description of how to use :func:`LoadAlignment` please refer to
:func:`LoadSequence`. For a list of file formats supported by
:func:`LoadAlignment` see :doc:`sequence_formats`.
+ :param filename: The filename
+ :type filename: string
+ :param format: Name of the format
+ :type format: string
+ :rtype: :class:`~ost.seq.AlignmentHandle`
+
.. function:: LoadSequenceProfile(filename, format='auto')
Load sequence profile data from disk. If format is set to 'auto', the function
@@ -226,6 +244,11 @@ Loading sequence or alignment files
For a list of file formats supported by :func:`LoadSequenceProfile` see
:doc:`sequence_profile_formats`.
+
+ :param filename: The filename
+ :type filename: string
+ :param format: Name of the format
+ :type format: string
:rtype: :class:`~ost.seq.ProfileHandle`
@@ -237,14 +260,44 @@ Loading sequence or alignment files
inexistent file.
.. function:: AlignmentFromString(data, format)
+
+ Load alignment from string.
+
+ The format argument is mandatory. For a list of supported formats,
+ see :doc:`sequence_formats`.
+
+ :param data: The alignment
+ :type data: string
+ :param format: Name of the format
+ :type format: string
+ :rtype: :class:`~ost.seq.AlignmentHandle`
+
.. function:: SequenceFromString(data, format)
+
+ Load sequence from string.
+
+ The format argument is mandatory. For a list of supported formats,
+ see :doc:`sequence_formats`.
+
+ :param data: The sequence
+ :type data: string
+ :param format: Name of the format
+ :type format: string
+ :rtype: :class:`~ost.seq.SequenceHandle`
+
.. function:: SequenceListFromString(data, format)
- Load alignment, sequence or list of sequences from string.
+ Load a list of sequences from string.
The format argument is mandatory. For a list of supported formats,
see :doc:`sequence_formats`.
+ :param data: The list of sequences
+ :type data: string
+ :param format: Name of the format
+ :type format: string
+ :rtype: :class:`~ost.seq.SequenceList`
+
Saving Sequence Data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -265,7 +318,14 @@ Saving Sequence Data
For a list of file formats supported by :func:`SaveSequence` see
:doc:`sequence_formats`.
-
+
+ :param sequence: The sequence
+ :type sequence: :class:`~ost.seq.SequenceHandle`
+ :param filename: The filename
+ :type filename: string
+ :param format: Name of the format
+ :type format: string
+
:raises: :exc:`~ost.io.IOUnknownFormatException` if the format string supplied
is not recognized or the file format can not be detected based on the
file extension.
@@ -279,6 +339,13 @@ Saving Sequence Data
:func:`SaveSequence`. For a list of file formats supported by
:func:`SaveSequenceList` see :doc:`sequence_formats`.
+ :param seq_list: The sequence list
+ :type seq_list: :class:`~ost.seq.SequenceList`
+ :param filename: The filename
+ :type filename: string
+ :param format: Name of the format
+ :type format: string
+
.. function:: SaveAlignment(aln, filename, format='auto')
For a desription of how to use :func:`SaveAlignment` please refer to
@@ -287,15 +354,52 @@ Saving Sequence Data
For a list of file formats supported by :func:`SaveAlignment` see
:doc:`sequence_formats`.
+ :param aln: The alignment
+ :type aln: :class:`~ost.seq.AlignmentHandle`
+ :param filename: The filename
+ :type filename: string
+ :param format: Name of the format
+ :type format: string
+
.. function:: AlignmentToString(ali, format)
+
+ Return alignment as a string.
+
+ The format argument is mandatory. For a list of supported formats
+ see :doc:`sequence_formats`.
+
+ :param ali: The alignment
+ :type ali: :class:`~ost.seq.AlignmentHandle`
+ :param format: Name of the format
+ :type format: string
+ :rtype: string
+
.. function:: SequenceToString(seq, format)
+
+ Return sequence as a string.
+
+ The format argument is mandatory. For a list of supported formats
+ see :doc:`sequence_formats`.
+
+ :param seq: The sequence
+ :type seq: :class:`~ost.seq.SequenceHandle`
+ :param format: Name of the format
+ :type format: string
+ :rtype: string
+
.. function:: SequenceListToString(seq_list, format)
- Return alignment, sequence or sequence list as a string.
+ Return sequence list as a string.
The format argument is mandatory. For a list of supported formats
see :doc:`sequence_formats`.
+ :param seq_list: The sequence list
+ :type seq: :class:`~ost.seq.SequenceList`
+ :param format: Name of the format
+ :type format: string
+ :rtype: string
+
.. _img-io:
Density Maps
--
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