diff --git a/modules/index.rst b/modules/index.rst
index 912fcdaed5a0f07b6843a114ed6da669f23c3207..f664be809700225a527c9c342483d6ed7c7b18e9 100644
--- a/modules/index.rst
+++ b/modules/index.rst
@@ -96,7 +96,7 @@ Varia
**Datasets:** :doc:`tabular data <table>`
-**Supported File Formats:** :doc:`structure formats<io/structure_formats>` | :doc:`sequence formats <io/sequence_formats>` | :doc:`image formats <io/image_formats>`
+**Supported File Formats:** :doc:`structure formats<io/structure_formats>` | :doc:`sequence formats <io/sequence_formats>` | :doc:`sequence profile formats <io/sequence_profile_formats>` | :doc:`image formats <io/image_formats>`
**Users** :doc:`Reporting a problem <users>`
diff --git a/modules/io/doc/io.rst b/modules/io/doc/io.rst
index 8d6cee55047692afa3ff20b6f1734fb5266c0e43..9b40234d5084fec0f9a8d58d8ab48bba5a0ef926 100644
--- a/modules/io/doc/io.rst
+++ b/modules/io/doc/io.rst
@@ -157,16 +157,49 @@ Loading sequence or alignment files
.. function:: LoadSequenceList(filename, format='auto')
- For a desription of how to use :func:`LoadSequenceList` please refer to
+ For a description of how to use :func:`LoadSequenceList` please refer to
:func:`LoadSequence`. For a list of file formats supported by
:func:`LoadSequenceList` see :doc:`sequence_formats`.
.. function:: LoadAlignment(filename, format='auto')
- For a desription of how to use :func:`LoadAlignment` please refer to
+ 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`.
+
+.. function:: LoadSequenceProfile(filename, format='auto')
+
+ Load sequence profile data from disk. If format is set to 'auto', the function
+ guesses the filetype based on the extension of the file. Files ending in
+ '.hhm' (output of HHblits) and '.pssm' (ASCII Table (PSSM) output of PSI-BLAST
+ as generated with blastpgp and flag -Q) will automatically be loaded.
+
+ For files with non-standard extensions, the format can be set explicitly
+ specifying the `format` parameter.
+
+ .. code-block:: python
+
+ # recognizes hhm file by file extension
+ myprof = io.LoadSequenceProfile('myhmm.hhm')
+ # recognizes pssm file by file extension
+ myprof = io.LoadSequenceProfile('myprof.pssm')
+
+ # to override format
+ myprof = io.LoadSequenceProfile('myfile', format='hhm')
+ myprof = io.LoadSequenceProfile('myfile', format='pssm')
+
+ For a list of file formats supported by :func:`LoadSequenceProfile` see
+ :doc:`sequence_profile_formats`.
+
+ :rtype: :class:`~ost.seq.ProfileHandle`
+
+ :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.
+ :exc:`~ost.io.IOException` if the import fails due to an erroneous or
+ inexistent file.
+
Saving Sequence Data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -247,7 +280,7 @@ Loading Density Maps
# recognizes mrc file by file extension
ent = io.LoadImage('file.mrc')
- # it is always possible to explicitely set the image format
+ # it is always possible to explicitly set the image format
# DAT file explicitly
ent = io.LoadImage('file', Dat())
diff --git a/modules/io/doc/sequence_profile_formats.rst b/modules/io/doc/sequence_profile_formats.rst
new file mode 100644
index 0000000000000000000000000000000000000000..8c14c7d7f8ad7f5003d700d7edc060b48da119ec
--- /dev/null
+++ b/modules/io/doc/sequence_profile_formats.rst
@@ -0,0 +1,23 @@
+Supported Sequence Profile File Formats
+================================================================================
+
+HHblits output
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+*Recognized File Extensions*
+ .hhm, .hhm.gz
+
+*Format Name*
+ hhm
+
+
+PSI-BLAST output
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+ASCII Table (PSSM) output of PSI-BLAST as generated with blastpgp and flag -Q.
+
+*Recognized File Extensions*
+ .pssm, .pssm.gz
+
+*Format Name*
+ pssm
diff --git a/modules/seq/base/doc/seq.rst b/modules/seq/base/doc/seq.rst
index c370c1a4015b9759912b5fb47dd5d4f401c7bb65..5022c0aba584d651d8e0d0d056e89cbc635468ff 100644
--- a/modules/seq/base/doc/seq.rst
+++ b/modules/seq/base/doc/seq.rst
@@ -438,17 +438,22 @@ an alignment:
Remove sequence at *index* from the alignment.
-Handling Hidden Markov Models
+Handling Sequence Profiles
--------------------------------------------------------------------------------
-The HMM provides a simple container for hidden markov models in form of
-single columns containing amino acid frequencies and transition probabilities.
+The :class:`ProfileHandle` provides a simple container for profiles for each
+residue. It mainly contains:
-.. class:: HMMColumn
+- *N* :class:`ProfileColumn` objects (*N* = number of residues in sequence)
+ which each contains 20 amino acid frequencies
+- a :attr:`~ProfileHandle.sequence` (:class:`str`) of length *N*
+- a :attr:`~ProfileHandle.null_model` to use for this profile
+
+.. class:: ProfileColumn
.. method:: BLOSUMNullModel()
- Static method, that returns a new :class:`HMMColumn` with amino acid
+ Static method, that returns a new :class:`ProfileColumn` with amino acid
frequencies given from the BLOSUM62 substitution matrix.
.. method:: GetFreq(aa)
@@ -465,75 +470,72 @@ single columns containing amino acid frequencies and transition probabilities.
:type aa: :class:`str`
:type freq: :class:`float`
- .. method:: GetTransitionFreq(from,to)
-
- :param from: Current state of HMM (HMM_MATCH, HMM_INSERT or HMM_DELETE)
- :param to: Next state
-
- :returns: Frequency of given state transition
-
- .. method:: SetTransitionFreq(from,to,freq)
-
- :param from: Current state of HMM (HMM_MATCH, HMM_INSERT or HMM_DELETE)
- :param to: Next state
- :param freq: Frequency of transition
-
- .. attribute:: one_letter_code
-
- One letter code, this column is associated to
-
.. attribute:: entropy
Shannon entropy based on the columns amino acid frequencies
-.. class:: HMM
-
- .. method:: Load(filename)
+.. class:: ProfileHandle
- Static method to load an hmm in the hhm format as it is in use in the HHSuite.
+ .. method:: __len__()
+
+ Returns the length of the sequence for which we have profile.
- :param filename: Name of file to load
- :type filename: :class:`str`
+ :rtype: :class:`int`
.. method:: AddColumn(col)
Appends column in the internal column list.
:param col: Column to add
- :type col: :class:`HMMColumn`
+ :type col: :class:`ProfileColumn`
.. method:: Extract(from,to)
:param from: Col Idx to start from
- :param to: End Idx, not included in sub-HMM
+ :param to: End Idx, not included in sub-ProfileHandle
:type from: :class:`int`
:type to: :class:`int`
- :returns: sub-HMM as defined by given indices
+ :returns: sub-profile as defined by given indices
+ (:attr:`null_model` is copied)
+ :rtype: :class:`ProfileHandle`
+
+ :raises: :exc:`~exceptions.Error` if if *to* <= *from* or
+ *to* > :meth:`__len__`.
+
+ .. method:: SetSequence(sequence)
+
+ Sets :attr:`sequence`.
+
+ .. method:: SetNullModel(null_model)
+
+ Sets :attr:`null_model`.
.. attribute:: sequence
- Sequence of the columns
+ Sequence for which we have this profile.
+ Note: user must enforce consistency between sequence length and number of
+ profile columns.
.. attribute:: columns
- Iterable columns of the HMM
+ Iterable columns of the profile
.. attribute:: null_model
- Null model of the HMM
+ Null model of the profile
.. attribute:: avg_entropy
Average entropy of all the columns
-.. class:: HMMDB
+.. class:: ProfileDB
- A simple database to gather :class:`HMM` objects. It is possible
+ A simple database to gather :class:`ProfileHandle` objects. It is possible
to save them to disk in a compressed format with limited accuracy
- (4 digits for freq values).
+ (4 digits for each frequency).
.. method:: Save(filename)
@@ -548,32 +550,27 @@ single columns containing amino acid frequencies and transition probabilities.
:type filename: :class:`str`
:returns: The loaded database
- .. method:: AddHMM(name, hmm)
+ .. method:: AddProfile(name, prof)
- :param name: Name of HMM to be added
- :param hmm: HMM to be added
+ :param name: Name of profile to be added
+ :param prof: Profile to be added
:type name: :class:`str`
- :type hmm: :class:`HMM`
+ :type prof: :class:`ProfileHandle`
:raises: :class:`Exception` when filename is longer than 255 characters.
- .. method:: GetHMM(name)
+ .. method:: GetProfile(name)
- :param name: Name of HMM to be returned
+ :param name: Name of profile to be returned
:type name: :class:`str`
- :returns: The requested :class:`HMM`
- :raises: :class:`Exception` when no :class:`HMM` for **name** exists.
+ :returns: The requested :class:`ProfileHandle`
+ :raises: :class:`Exception` when no :class:`ProfileHandle` for **name** exists.
.. method:: Size()
- :returns: Number of :class:`HMM` objects in the database
+ :returns: Number of :class:`ProfileHandle` objects in the database
.. method:: GetNames()
- :returns: A nonsorted list of the names of all :class:`HMM` objects in the database
-
-
-
-
-
-
+ :returns: A nonsorted list of the names of all :class:`ProfileHandle`
+ objects in the database
diff --git a/modules/seq/base/pymod/export_profile_handle.cc b/modules/seq/base/pymod/export_profile_handle.cc
index 77479ac31876728d6edd62fcaf3259acc7c58d00..e563960f424e448863bf17f7d52d10db8b2875e5 100644
--- a/modules/seq/base/pymod/export_profile_handle.cc
+++ b/modules/seq/base/pymod/export_profile_handle.cc
@@ -60,6 +60,8 @@ void export_profile_handle()
.def("__len__",&ProfileHandle::size)
.def("AddColumn", &ProfileHandle::push_back)
.def("Extract", &ProfileHandle::Extract)
+ .def("SetNullModel", &ProfileHandle::SetNullModel)
+ .def("SetSequence", &ProfileHandle::SetSequence)
.add_property("null_model", make_function(&ProfileHandle::GetNullModel,
return_value_policy<copy_const_reference>()))
.add_property("columns",
diff --git a/modules/seq/base/src/profile_handle.hh b/modules/seq/base/src/profile_handle.hh
index e3642b6e16c45f8a10e9bba39dbbd29b04d4a91d..0d67f8c696a0995133473c2da7a979d8b84bd6bd 100644
--- a/modules/seq/base/src/profile_handle.hh
+++ b/modules/seq/base/src/profile_handle.hh
@@ -44,7 +44,7 @@ typedef boost::shared_ptr<ProfileHandle> ProfileHandlePtr;
typedef boost::shared_ptr<ProfileDB> ProfileDBPtr;
typedef std::vector<ProfileColumn> ProfileColumnList;
-/// \brief Defines profile of 20 frequencies for one residue.
+/// \brief Defines profile of 20 frequencies for one residue.
///
/// Frequencies are identified by the one-letter-code for that amino acid.
/// (possible codes: ACDEFGHIKLMNPQRSTVWY)