biotite 0.41.1__tar.gz → 0.41.2__tar.gz

{biotite-0.41.1 → biotite-0.41.2}/.gitignore

@@ -20,10 +20,9 @@ htmlcov
 # Ignore version file created by hatch-vcs
 /src/biotite/version.py
 
-# Ignore autogenerated API reference
+# Ignore autogenerated documentation files
+/doc/static/switcher.json
 /doc/apidoc
-
-# Ignore autogenerated example gallery
 /doc/examples/gallery
 /doc/examples/backreferences
 /doc/sg_execution_times.rst
@@ -58,8 +57,9 @@ biotite.egg-info
 *.code-workspace
 .vscode/*
 
-# Ignore fuse_hidden files on Linux systems
+# Ignore hidden OS related files
 *.fuse_hidden*
+.DS_Store
 
 # Ignore temp files created via Jupyter
 **/.ipynb_checkpoints/

{biotite-0.41.1 → biotite-0.41.2}/CONTRIB.rst

@@ -4,6 +4,7 @@ CONTRIBUTORS
 - Fabrice Allain <https://github.com/f-allain>
 - Jacob Marcel Anter <https://github.com/JacobAnter>
 - Daniel Bauer <https://github.com/dnlbauer>
+- Lukas Jarosch <https://github.com/ljarosch>
 - Patrick Kunzmann <https://github.com/padix-key>
 - Tom David Müller <https://github.com/t0mdavid-m>
 - Thomas Nevolianis <https://github.com/thomasnevolianis>

{biotite-0.41.1 → biotite-0.41.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: biotite
-Version: 0.41.1
+Version: 0.41.2
 Summary: A comprehensive library for computational molecular biology
 Project-URL: homepage, https://www.biotite-python.org
 Project-URL: repository, https://github.com/biotite-dev/biotite
@@ -184,4 +184,4 @@ Contribution
 Interested in improving *Biotite*?
 Have a look at the
 `contribution guidelines <https://www.biotite-python.org/contribute.html>`_.
-Feel free to join or community chat on `Discord <https://discord.gg/cUjDguF>`_.
+Feel free to join our community chat on `Discord <https://discord.gg/cUjDguF>`_.

{biotite-0.41.1 → biotite-0.41.2}/README.rst

@@ -125,4 +125,4 @@ Contribution
 Interested in improving *Biotite*?
 Have a look at the
 `contribution guidelines <https://www.biotite-python.org/contribute.html>`_.
-Feel free to join or community chat on `Discord <https://discord.gg/cUjDguF>`_.
+Feel free to join our community chat on `Discord <https://discord.gg/cUjDguF>`_.

{biotite-0.41.1 → biotite-0.41.2}/pyproject.toml

@@ -45,7 +45,9 @@ exclude = [
   "tests",
   "doc",
   "environment.yml",
-  "setup_ccd.py"
+  "setup_ccd.py",
+  # .github, .gitignore, .gitattributes
+  ".git*",
 ]
 
 [tool.hatch.version]

biotite-0.41.2/src/biotite/application/__init__.py

@@ -0,0 +1,69 @@
+# This source code is part of the Biotite package and is distributed
+# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
+# information.
+
+"""
+A subpackage that provides interfaces for external software in case
+*Biotite*’s integrated functionality is not sufficient for your tasks.
+These interfaces range from locally installed software
+(e.g. MSA software) to web services (e.g. BLAST).
+The interfaces are seamless:
+Writing input files and reading output files is handled internally.
+The user only needs to provide objects like a :class:`Sequence`
+and will receive objects like an :class:`Alignment`.
+
+Note that in order to use an interface in :mod:`biotite.application`
+the corresponding software must be installed or the web server must be
+reachable, respectively.
+These programs are not shipped with the *Biotite* package.
+
+Each application is represented by its respective :class:`Application`
+class.
+Each :class:`Application` instance has a life cycle, starting with its
+creation and ending with the result extraction.
+Each state in this life cycle is described by the value of the
+*enum* :class:`AppState`, that each :class:`Application` contains:
+Directly after its instantiation the app is in the ``CREATED`` state.
+In this state further parameters can be set for the application run.
+After the user calls the :func:`Application.start()` method, the app
+state is set to ``RUNNING`` and the app performs the calculations.
+When the application finishes the AppState
+changes to ``FINISHED``.
+The user can now call the :func:`Application.join()` method, concluding
+the application in the ``JOINED`` state and making the results of the
+application accessible.
+Furthermore, this may trigger cleanup actions in some applications.
+:func:`Application.join()` can even be called in the ``RUNNING`` state:
+This will constantly check if the application has finished and will
+directly go into the ``JOINED`` state as soon as the application reaches
+the ``FINISHED`` state.
+Calling the :func:`Application.cancel()` method while the application is
+``RUNNING`` or ``FINISHED`` leaves the application in the ``CANCELLED``
+state.
+This triggers cleanup, too, but there are no accessible results.
+If a method is called in an unsuitable app state, an
+:class:`AppStateError` is called.
+At each state in the life cycle, :class:`Application` type specific
+methods are called, as shown in the following diagram.
+
+.. figure:: /static/assets/figures/app_lifecycle.png
+    :alt: Application life cycle
+    :scale: 50%
+
+    Taken from
+    `Kunzmann & Hamacher 2018 <https://doi.org/10.1186/s12859-018-2367-z>`_
+    licensed under `CC BY 4.0 <https://creativecommons.org/licenses/by/4.0/>`_.
+
+The execution of an :class:`Application` can run in parallel:
+The time between starting the run and collecting the results can be
+used to run other code, similar to the *Python* :class:`Thread` or
+:class:`Process` classes.
+"""
+
+__name__ = "biotite.application"
+__author__ = "Patrick Kunzmann"
+
+from .application import *
+from .localapp import *
+from .webapp import *
+from .msaapp import *

{biotite-0.41.1 → biotite-0.41.2}/src/biotite/application/application.py

@@ -74,7 +74,8 @@ class Application(metaclass=abc.ABCMeta):
 
     Every :class:`Application` runs through a different app states
     (instances of enum :class:`AppState`) from its creation until its
-    termination:
+    termination.
+
     Directly after its instantiation the app is in the *CREATED* state.
     In this state further parameters can be set for the application run.
     After the user calls the :func:`start()` method, the app state is

{biotite-0.41.1 → biotite-0.41.2}/src/biotite/sequence/__init__.py

@@ -24,7 +24,15 @@ For example, ``'A'``, ``'C'``, ``'G'`` and ``'T'`` would be encoded into
 These integer values are called *symbol code*, the encoding of an entire
 sequence of symbols is called *sequence code*.
 
-The size of the symbol code type in the array is determined by the 
+.. figure:: /static/assets/figures/symbol_encoding.png
+    :alt: Symbol encoding in Biotite
+    :scale: 50%
+
+    Taken from
+    `Kunzmann & Hamacher 2018 <https://doi.org/10.1186/s12859-018-2367-z>`_
+    licensed under `CC BY 4.0 <https://creativecommons.org/licenses/by/4.0/>`_.
+
+The size of the symbol code type in the array is determined by the
 size of the :class:`Alphabet`:
 If the :class:`Alphabet` contains 256 symbols or less, one byte is used
 per array element, between 257 and 65536 symbols, two bytes are used,
@@ -41,6 +49,7 @@ This approach has multiple advantages:
       indifferent to the actual type of sequence.
     - Symbol codes are directly indices for substitution matrices in
       alignments
+    - *k-mers* can be computed fast
 
 The abstract :class:`Sequence` superclass cannot be instantiated
 directly, as it does not define an :class:`Alphabet` by itself.
@@ -55,10 +64,12 @@ The class :class:`GeneralSequence` allows the usage of a custom
 Additionally, this subpackage provides support for sequence features,
 as used in e.g. GenBank or GFF files.
 A :class:`Feature` stores its key name, its qualifiers and locations.
-An :class:`Annotation` is a group of multiple :class:`Feataure` objects
+An :class:`Annotation` is a group of multiple :class:`Feature` objects
 and offers convenient location based indexing.
 An :class:`AnnotatedSequence` combines an :class:`Annotation` and a
 :class:`Sequence`.
+
+Sequence profiles can be created with the :class:`SequenceProfile` class.
 """
 
 __name__ = "biotite.sequence"

biotite-0.41.2/src/biotite/sequence/align/__init__.py

@@ -0,0 +1,203 @@
+# This source code is part of the Biotite package and is distributed
+# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
+# information.
+
+"""
+This subpackage provides functionality for sequence alignments.
+
+The two central classes involved are :class:`SubstitutionMatrix` and
+:class:`Alignment`:
+
+Every function that performs an alignment requires a
+:class:`SubstitutionMatrix` that provides similarity scores for each
+symbol combination of two alphabets (usually both alphabets are equal).
+The alphabets in the :class:`SubstitutionMatrix` must match or extend
+the alphabets of the sequences to be aligned.
+
+An alignment cannot be directly represented as list of :class:`Sequence`
+objects, since a gap indicates the absence of any symbol.
+Instead, the aligning functions return one or more :class:`Alignment`
+instances.
+These objects contain the original sequences and a trace, that describe
+which positions (indices) in the sequences are aligned.
+Optionally they also contain the similarity score.
+
+The aligning functions :func:`align_optimal()` and
+:func:`align_multiple()` cover most use cases for pairwise and multiple
+sequence alignments respectively.
+
+However, *Biotite* provides also a modular system to build performant
+heuristic alignment search methods, e.g. for finding homologies in a sequence
+database or map reads to a genome.
+The table below summarizes those provided functionalities.
+The typical stages in alignment search, where those functionalities are used,
+are arranged from top to bottom.
+
+.. grid::
+    :gutter: 0
+    :class-container: sd-text-center
+
+    .. grid-item::
+        :padding: 2
+        :outline:
+        :columns: 3
+
+        **Entire k-mer set**
+
+    .. grid-item::
+        :padding: 2
+        :outline:
+        :columns: 9
+
+        .. grid::
+            :margin: 0
+
+            .. grid-item::
+                :padding: 2
+                :columns: 12
+
+                **k-mer subset selection**
+
+            .. grid-item::
+                :padding: 2
+                :columns: 4
+
+                Minimizers
+
+                :class:`MinimizerSelector`
+
+            .. grid-item::
+                :padding: 2
+                :columns: 4
+
+                Syncmers
+
+                :class:`SyncmerSelector`
+
+                :class:`CachedSyncmerSelector`
+
+            .. grid-item::
+                :padding: 2
+                :columns: 4
+
+                Mincode
+
+                :class:`MincodeSelector`
+
+
+    .. grid-item::
+        :padding: 2
+        :outline:
+        :columns: 12
+
+        .. grid::
+            :margin: 0
+
+            .. grid-item::
+                :padding: 2
+                :columns: 12
+
+                **k-mer indexing and matching**
+
+            .. grid-item::
+                :padding: 2
+                :columns: 6
+
+                Perfect hashing
+
+                :class:`KmerTable`
+
+            .. grid-item::
+                :padding: 2
+                :columns: 6
+
+                Space-efficient hashing
+
+                :class:`BucketKmerTable`
+
+                :func:`bucket_number()`
+
+
+    .. grid-item::
+        :padding: 2
+        :outline:
+        :columns: 12
+
+        .. grid::
+            :margin: 0
+
+            .. grid-item::
+                :padding: 2
+                :columns: 12
+
+                **Ungapped seed extension**
+
+                :class:`align_local_ungapped()`
+
+
+    .. grid-item::
+        :padding: 2
+        :outline:
+        :columns: 12
+
+        .. grid::
+            :margin: 0
+
+            .. grid-item::
+                :padding: 2
+                :columns: 12
+
+                **Gapped alignment**
+
+            .. grid-item::
+                :padding: 2
+                :columns: 6
+
+                Banded local/semiglobal alignment
+
+                :class:`align_banded()`
+
+            .. grid-item::
+                :padding: 2
+                :columns: 6
+
+                Local alignment (*X-drop*)
+
+                :class:`align_local_gapped()`
+
+    .. grid-item::
+        :padding: 2
+        :outline:
+        :columns: 12
+
+        .. grid::
+            :margin: 0
+
+            .. grid-item::
+                :padding: 2
+                :columns: 12
+
+                **Significance evaluation**
+
+                :class:`EValueEstimator`
+
+"""
+
+__name__ = "biotite.sequence.align"
+__author__ = "Patrick Kunzmann"
+
+from .alignment import *
+from .banded import *
+from .buckets import *
+from .cigar import *
+from .kmeralphabet import *
+from .kmertable import *
+from .kmersimilarity import *
+from .localgapped import *
+from .localungapped import *
+from .matrix import *
+from .multiple import *
+from .pairwise import *
+from .permutation import *
+from .selector import *
+from .statistics import *

{biotite-0.41.1 → biotite-0.41.2}/src/biotite/sequence/align/multiple.pyx

@@ -39,9 +39,9 @@ cdef float32 MAX_FLOAT = np.finfo(np.float32).max
 
 
 class GapSymbol:
-    
+
     _instance = None
-    
+
     def __init__(self):
         if GapSymbol._instance is not None:
             raise ValueError(
@@ -49,16 +49,16 @@ class GapSymbol:
             )
         else:
             GapSymbol._instance = self
-    
+
     @staticmethod
     def instance():
         if GapSymbol._instance is None:
             GapSymbol._instance = GapSymbol()
         return GapSymbol._instance
-    
+
     def __str__(self):
         return "-"
-    
+
     def __hash__(self):
         return 0
 
@@ -69,13 +69,13 @@ def align_multiple(sequences, matrix, gap_penalty=-10, terminal_penalty=True,
     align_multiple(sequences, matrix, gap_penalty=-10,
                    terminal_penalty=True, distances=None,
                    guide_tree=None)
-    
+
     Perform a multiple sequence alignment using a progressive
     alignment algorithm. :footcite:`Feng1987`
 
     Based on pairwise sequence distances a guide tree is constructed.
     The sequences are progessively aligned according to the tree,
-    following the rule 'Once a gap, always a gap'. 
+    following the rule 'Once a gap, always a gap'.
 
     Parameters
     ----------
@@ -124,7 +124,7 @@ def align_multiple(sequences, matrix, gap_penalty=-10, terminal_penalty=True,
     distance_matrix : ndarray, shape=(n,n), dtype=float32
         The pairwise distance matrix used to construct the guide tree.
         Equal to `distances` if provided.
-    
+
     Notes
     -----
     The similarity to distance conversion is performed according to the
@@ -137,14 +137,14 @@ def align_multiple(sequences, matrix, gap_penalty=-10, terminal_penalty=True,
               \right)
 
     .. math:: S_{a,b}^{max} = \frac{ S_{a,a} + S_{b,b} }{ 2 }
-    
+
     .. math:: S_{a,b}^{rand} = \frac{1}{L_{a,b}}
               \left(
                  \sum_{x \in \Omega} \sum_{y \in \Omega}
                  s_{x,y} \cdot N_a(x) \cdot N_b(y)
               \right)
               + N_{a,b}^{open} \cdot p^{open} + N_{a,b}^{ext} \cdot p^{ext}
-    
+
     :math:`D_{a,b}` - The distance between the sequences *a* and *b*.
 
     :math:`S_{a,b}` - The similarity score between the sequences *a* and *b*.
@@ -164,17 +164,17 @@ def align_multiple(sequences, matrix, gap_penalty=-10, terminal_penalty=True,
 
     In rare cases of extremely unrelated sequences, :math:`S_{a,b}`
     can be lower than :math:`S_{a,b}^{rand}`.
-    In this case the logaritmus cannot be calculated and a
+    In this case the logarithm cannot be calculated and a
     :class:`ValueError` is raised.
 
     References
     ----------
-    
+
     .. footbibliography::
 
     Examples
     --------
-    
+
     >>> seq1 = ProteinSequence("BIQTITE")
     >>> seq2 = ProteinSequence("TITANITE")
     >>> seq3 = ProteinSequence("BISMITE")
@@ -232,7 +232,7 @@ def align_multiple(sequences, matrix, gap_penalty=-10, terminal_penalty=True,
     else:
         # Assure that every node in the guide tree is binary
         guide_tree = as_binary(guide_tree)
-    
+
     # Create new matrix with neutral gap symbol
     gap_symbol = GapSymbol.instance()
     new_alphabet = Alphabet(
@@ -275,7 +275,7 @@ def align_multiple(sequences, matrix, gap_penalty=-10, terminal_penalty=True,
     ]
     for i in range(len(aligned_seqs)):
         aligned_seqs[i].code = aligned_seq_codes[i]
-    
+
     # Reorder alignmets into original alignemnt
     new_order = np.argsort(order)
     aligned_seqs = [aligned_seqs[pos] for pos in new_order]
@@ -290,7 +290,7 @@ def _get_distance_matrix(CodeType[:] _T, sequences, matrix,
     Create all pairwise alignments for the given sequences and use the
     method proposed by Feng & Doolittle to calculate the pairwise
     distance matrix
-    
+
     Parameters
     ----------
     _T : ndarray, dtype=VARAIBLE
@@ -306,7 +306,7 @@ def _get_distance_matrix(CodeType[:] _T, sequences, matrix,
     terminal_penalty : bool
         Whether to or not count terminal gap penalties for the
         alignments.
-    
+
     Returns
     -------
     distances : ndarray, shape=(n,n), dtype=float32
@@ -332,7 +332,7 @@ def _get_distance_matrix(CodeType[:] _T, sequences, matrix,
             )[0]
             scores[i,j] = alignment.score
             alignments[i,j] = alignment
-    
+
     ### Distance calculation from similarity scores ###
     # Calculate the occurences of each symbol code in each sequence
     # This is used later for the random score
@@ -364,7 +364,7 @@ def _get_distance_matrix(CodeType[:] _T, sequences, matrix,
     cdef CodeType[:] seq_code1, seq_code2
     cdef CodeType code1, code2
     cdef float32 score_rand, score_max
-    
+
     # Calculate distance
     # i and j are indicating the alignment between the sequences i and j
     for i in range(scores_v.shape[0]):
@@ -405,14 +405,14 @@ def _count_gaps(int64[:,:] trace_v, bint terminal_penalty):
     """
     Count the number of gap openings and gap extensions in an alignment
     trace.
-    
+
     Parameters
     ----------
     trace_v : ndarary, shape=(n,2), dtype=int
         The alignemnt trace.
     terminal_penalty : bool
         Whether to or not count terminal gap penalties.
-    
+
     Returns
     -------
     gap_open_count, gap_ext_count: int
@@ -440,7 +440,7 @@ def _count_gaps(int64[:,:] trace_v, bint terminal_penalty):
         if start_index == -1 or stop_index == -1:
             return 0, 0
         trace_v = trace_v[start_index : stop_index]
-    
+
     if trace_v[0,0] == -1:
         gap_open_count += 1
     if trace_v[0,1] == -1:
@@ -471,7 +471,7 @@ def _progressive_align(CodeType[:] _T, sequences, tree_node,
     The gaps inserted in this pairwise alignment are also inserted
     into all other sequences in the respective sub-MSA at the same
     position.
-    
+
     Parameters
     ----------
     _T : ndarray, dtype=VARAIBLE
@@ -490,13 +490,13 @@ def _progressive_align(CodeType[:] _T, sequences, tree_node,
     matrix : SubstitutionMatrix
         The substitution matrix used for the alignments.
     gap_symbol_code : int
-        The symbol code for the gap symbol. 
+        The symbol code for the gap symbol.
     gap_penalty : int or tuple(int, int)
         A linear or affine gap penalty for the alignments.
     terminal_penalty : bool
         Whether to or not count terminal gap penalties for the
         alignments.
-    
+
     Returns
     -------
     order : ndarray, shape=(m,), dtype=int
@@ -515,7 +515,7 @@ def _progressive_align(CodeType[:] _T, sequences, tree_node,
     cdef int32[:] indices1_v, indices2_v
     cdef np.ndarray incides1, incides2
     cdef list aligned_seqs1, aligned_seqs2
-    
+
     if tree_node.is_leaf():
         # Child node -> Cannot do an alignment
         # -> Just return the sequence corresponding to the leaf node
@@ -523,7 +523,7 @@ def _progressive_align(CodeType[:] _T, sequences, tree_node,
         # when neutral gap character is inserted
         return np.array([tree_node.index], dtype=np.int32), \
                [sequences[tree_node.index].copy()]
-    
+
     else:
         # Multiple alignment of sequences corresponding to both child nodes
         child1, child2 = tree_node.children
@@ -537,7 +537,7 @@ def _progressive_align(CodeType[:] _T, sequences, tree_node,
             gap_symbol_code, gap_penalty, terminal_penalty
         )
         indices2_v = incides2
-        
+
         # Find sequence pair with lowest distance
         dist_min = MAX_FLOAT
         for i in range(indices1_v.shape[0]):
@@ -554,7 +554,7 @@ def _progressive_align(CodeType[:] _T, sequences, tree_node,
             gap_penalty, terminal_penalty, max_number=1
         )[0]
         # Place neutral gap symbol for position of new gaps
-        # in both sequence groups 
+        # in both sequence groups
         for i in range(len(aligned_seqs1)):
             seq = aligned_seqs1[i]
             seq.code = _replace_gaps(
@@ -580,7 +580,7 @@ def _replace_gaps(CodeType[:] _T,
 
     The replacement is required by the progressive alignment algorithm
     to be able to align gapped sequences with each other.
-    
+
     Parameters
     ----------
     _T : ndarray, dtype=VARAIBLE
@@ -592,8 +592,8 @@ def _replace_gaps(CodeType[:] _T,
     seq_code : ndarary, shape=(n,)
         The sequence code representing the given sequence.
     gap_symbol_code : int
-        The symbol code for the gap symbol. 
-    
+        The symbol code for the gap symbol.
+
     Returns
     -------
     new_seq_code : ndarary, shape=(m,)
@@ -609,12 +609,12 @@ def _replace_gaps(CodeType[:] _T,
         partial_trace_v.shape[0], dtype=seq_code.dtype
     )
     cdef CodeType[:] new_seq_code_v = new_seq_code
-    
+
     for i in range(partial_trace_v.shape[0]):
         index = partial_trace_v[i]
         if index == -1:
             new_seq_code_v[i] = gap_symbol_code
         else:
             new_seq_code_v[i] = seq_code[index]
-    
+
     return new_seq_code