dnachisel - pypi Package Compare versions

Comparing version 3.2.10 to 3.2.11

dnachisel.egg-info/PKG-INFO

 Metadata-Version: 2.1
 Name: dnachisel
-Version: 3.2.10
+Version: 3.2.11
 Summary: Optimize DNA sequences under constraints.
@@ -11,2 +11,3 @@ Home-page: https://github.com/Edinburgh-Genome-Foundry/DnaChisel
 Provides-Extra: reports
+Provides-Extra: tests
 License-File: LICENCE.txt
@@ -13,0 +14,0 @@

dnachisel.egg-info/requires.txt

@@ -14,1 +14,10 @@ numpy
 pandas
+
+[tests]
+pytest
+pytest-cov
+coveralls
+geneblocks
+genome_collector
+matplotlib
+primer3-py

dnachisel/biotools/biotables.py

@@ -52,2 +52,4 @@ """This module provides useful biological tables as Python dictionaries.
 
+def flatten(l):
+    return [item for sublist in l for item in sublist]
 
@@ -63,2 +65,6 @@ def get_backtranslation_table(table_name="Standard"):
     back_translation_table["START"] = table.start_codons
+    back_translation_table["X"] = list(set(flatten(back_translation_table.values())) - set(back_translation_table["*"]))
+    back_translation_table["B"] = back_translation_table["N"] + back_translation_table["D"]
+    back_translation_table["J"] = back_translation_table["L"] + back_translation_table["I"]
+    back_translation_table["Z"] = back_translation_table["E"] + back_translation_table["Q"]
     return back_translation_table

dnachisel/biotools/genbank_operations.py

@@ -126,3 +126,3 @@ """Generic methods for reading/modifying Genbank/Biopython records"""
     new_record = deepcopy(record)
-    for (start, end) in locations:
+    for start, end in locations:
         annotate_record(
@@ -148,3 +148,3 @@ new_record,
     pattern
-      A DnaChisel SequencePattern object (such as DnaPAttern).
+      A DNA Chisel SequencePattern object. See SequencePattern documentation.
 
@@ -151,0 +151,0 @@ feature_type

dnachisel/builtin_specifications/AvoidPattern.py

@@ -18,3 +18,5 @@ """Implement AvoidPattern"""
     pattern
-      A SequencePattern or DnaNotationPattern
+      A SequencePattern or DnaNotationPattern. If a ``str`` is given, it will
+      be converted. Note that providing ``size`` may be necessary for certain
+      patterns. See SequencePattern documentation for more details.
 
@@ -21,0 +23,0 @@ location

dnachisel/builtin_...s/codon_optimization/AvoidRareCodons.py

@@ -32,4 +32,5 @@ "Implement AvoidRareCodons."
       codon-optimized, which can be provided instead of ``species``. A dict of
-      the form ``{'*': {"TGA": 0.112, "TAA": 0.68}, 'K': ...}`` giving the RSCU
-      table (relative usage of each codon). See parameter ``species`` above.
+      the form ``{'*': {"TGA": 0.112, "TAA": 0.68}, 'K': ...}`` giving the codon
+      frequency table (relative usage of each codon; frequencies add up to 1,
+      separately for each amino acid). See parameter ``species`` above.
 
@@ -36,0 +37,0 @@ location

dnachisel/builtin_...ons/codon_optimization/CodonOptimize.py

@@ -58,4 +58,5 @@ from .HarmonizeRCA import HarmonizeRCA
       codon-optimized, which can be provided instead of ``species``. A dict of
-      the form ``{'*': {"TGA": 0.112, "TAA": 0.68}, 'K': ...}`` giving the RSCU
-      table (relative usage of each codon). See parameter ``species`` above.
+      the form ``{'*': {"TGA": 0.112, "TAA": 0.68}, 'K': ...}`` giving the codon
+      frequency table (relative usage of each codon; frequencies add up to 1,
+      separately for each amino acid). See parameter ``species`` above.
 
@@ -62,0 +63,0 @@ original_species

dnachisel/builtin_...ions/codon_optimization/HarmonizeRCA.py

@@ -42,4 +42,5 @@ import numpy as np
       Optional - can be provided instead of ``species``. A dict of the form
-      ``{'*': {"TGA": 0.112, "TAA": 0.68}, 'K': ...}`` giving the RSCU table
-      (relative usage of each codon).
+      ``{'*': {"TGA": 0.112, "TAA": 0.68}, 'K': ...}`` giving the codon
+      frequency table (relative usage of each codon; frequencies add up to 1,
+      separately for each amino acid).
 
@@ -54,3 +55,4 @@ original_species
       A dict of the form ``{'*': {"TGA": 0.112, "TAA": 0.68}, 'K': ...}``
-      giving the RSCU table (relative usage of each codon).
+      giving the codon frequency table (relative usage of each codon;
+      frequencies add up to 1, separately for each amino acid).
 
@@ -57,0 +59,0 @@ location

dnachisel/builtin_...n_optimization/MatchTargetCodonUsage.py

@@ -46,4 +46,5 @@ import numpy as np
       A dict of the form ``{'*': {"TGA": 0.112, "TAA": 0.68}, 'K': ...}``
-      giving the RSCU table (relative usage of each codon). Only provide if
-      no ``species`` parameter was provided.
+      giving the codon frequency table (relative usage of each codon;
+      frequencies add up to 1, separately for each amino acid). Only
+      provide if no ``species`` parameter was provided.
 
@@ -50,0 +51,0 @@ boost

dnachisel/builtin_...tions/codon_optimization/MaximizeCAI.py

@@ -46,4 +46,5 @@ import numpy as np
       A dict of the form ``{'*': {"TGA": 0.112, "TAA": 0.68}, 'K': ...}``
-      giving the RSCU table (relative usage of each codon). Only provide if
-      no ``species`` parameter was provided.
+      giving the codon frequency table (relative usage of each codon;
+      frequencies add up to 1, separately for each amino acid). Only
+      provide if no ``species`` parameter was provided.
 
@@ -50,0 +51,0 @@ boost

dnachisel/builtin_specifications/EnforcePatternOccurence.py

@@ -25,3 +25,3 @@ """Implement EnforcePatternOccurence"""
       A SequencePattern or DnaNotationPattern or a string such as "AATTG",
-      "BsmBI_site", etc.
+      "BsmBI_site", etc. See SequencePattern documentation for more details.
 
@@ -91,3 +91,6 @@ occurences
         """Score the difference between expected and observed n_occurences."""
-        matches = self.pattern.find_matches(problem.sequence, self.location,)
+        matches = self.pattern.find_matches(
+            problem.sequence,
+            self.location,
+        )
         score = -abs(len(matches) - self.occurences)
@@ -94,0 +97,0 @@

dnachisel/Location.py

@@ -6,3 +6,6 @@ """Implements the Location class.
 """
+from functools import total_ordering
 
+from Bio.SeqFeature import FeatureLocation, SeqFeature
+
 from .biotools import reverse_complement
@@ -12,2 +15,3 @@ from Bio.SeqFeature import SeqFeature, FeatureLocation
 
+@total_ordering
 class Location:
@@ -98,5 +102,5 @@ """Represent a segment of a sequence, with a start, end, and strand.
 
-    def __geq__(self, other):
-        """Greater than."""
-        return self.to_tuple() >= other.to_tuple()
+    def __eq__(self, other):
+        """Equal to."""
+        return self.to_tuple() == other.to_tuple()
 
@@ -126,2 +130,5 @@ def __lt__(self, other):
 
+    def __hash__(self):
+        return hash(self.to_tuple())
+
     @staticmethod
@@ -128,0 +135,0 @@ def merge_overlapping_locations(locations):

dnachisel/SequencePattern/SequencePattern.py

@@ -19,3 +19,3 @@ """Implements the SequencePattern, DnaNotationPattern classes.
 class SequencePattern:
-    """Pattern/ that will be looked for in a DNA sequence.
+    """Pattern that will be looked for in a DNA sequence.
 
@@ -36,18 +36,17 @@ Use this class for matching regular expression patterns, and
     expression
-      Any string or regular expression for matching ATGC nucleotides.
-      Note that multi-nucleotides symbols such as "N" (for A-T-G-C), or "K"
+      Any string or regular expression (regex) for matching ATGC nucleotides.
+      Note that multi-nucleotide symbols such as "N" (for A-T-G-C), or "K"
       are not supported by this class, see DnaNotationPattern instead.
 
     size
-      Size of the pattern, in number of characters (if none provided, the size
-      of the ``pattern`` string is used).
-      The ``size`` is used to determine the size of windows when performing
-      local optimization and constraint solving.
-      It can be important to provide the size when the
+      Size of the pattern, in number of characters. The ``size`` is used to
+      determine the size of windows when performing local optimization and
+      constraint solving. It can be important to provide the size when the
       ``pattern`` string provided represents a complex regular expression whose
       maximal matching size cannot be easily evaluated.
+      For example, if a regex is used to actively remove sites, then a size
+      should be provided to inform DNA Chisel during optimization.
 
     name
-      Name of the pattern (will be displayed e.g. when the pattern is printed)
-
+      Name of the pattern (will be displayed e.g. when the pattern is printed).
     """
@@ -105,7 +104,6 @@
         if forced_strand is not None:
-            subsequence = sequence[location.start: location.end]
+            subsequence = sequence[location.start : location.end]
             if forced_strand == 1:
                 return [
-                    (loc + location.start)
-                    for loc in self.find_matches(subsequence)
+                    (loc + location.start) for loc in self.find_matches(subsequence)
                 ]
@@ -135,3 +133,3 @@ if forced_strand == -1:
             if strand == 0:
-                matches =  self.find_matches(sequence, location, 1)
+                matches = self.find_matches(sequence, location, 1)
                 if not self.is_palyndromic:
@@ -165,5 +163,3 @@ matches += self.find_matches(sequence, location, -1)
     def __str__(self):
-        return self.expression + (
-            "" if self.name is None else " (%s)" % self.name
-        )
+        return self.expression + ("" if self.name is None else " (%s)" % self.name)
 
@@ -170,0 +166,0 @@ @classmethod

dnachisel/version.py

@@ -1,1 +0,1 @@
-__version__ = "3.2.10"
+__version__ = "3.2.11"

PKG-INFO

 Metadata-Version: 2.1
 Name: dnachisel
-Version: 3.2.10
+Version: 3.2.11
 Summary: Optimize DNA sequences under constraints.
@@ -11,2 +11,3 @@ Home-page: https://github.com/Edinburgh-Genome-Foundry/DnaChisel
 Provides-Extra: reports
+Provides-Extra: tests
 License-File: LICENCE.txt
@@ -13,0 +14,0 @@

README.rst

@@ -11,5 +11,5 @@ .. raw:: html
 
-.. image:: https://travis-ci.com/Edinburgh-Genome-Foundry/DnaChisel.svg?branch=master
-   :target: https://travis-ci.com/Edinburgh-Genome-Foundry/DnaChisel
-   :alt: Travis CI build status
+.. image:: https://github.com/Edinburgh-Genome-Foundry/DnaChisel/actions/workflows/build.yml/badge.svg
+   :target: https://github.com/Edinburgh-Genome-Foundry/DnaChisel/actions/workflows/build.yml
+   :alt: GitHub CI build status
 
@@ -114,6 +114,6 @@ .. image:: https://coveralls.io/repos/github/Edinburgh-Genome-Foundry/DnaChisel/badge.svg?branch=master
 
-By default, only the built-in specifications of DnaChisel can be used in the
+By default, only the built-in specifications of DNA Chisel can be used in the
 annotations, however it is easy to add your own specifications to the Genbank
 parser, and build applications supporting custom specifications on top of
-DnaChisel.
+DNA Chisel.
 
@@ -124,6 +124,7 @@
 
-DnaChisel also implements features for verification and troubleshooting. For
+DNA Chisel also implements features for verification and troubleshooting. For
 instance by generating optimization reports:
 
 .. code:: python
+
     problem = DnaOptimizationProblem(...)
@@ -147,3 +148,3 @@ problem.optimize_with_report(target="report.zip")
 
-DnaChisel hunts down every constraint breach and suboptimal region by
+DNA Chisel hunts down every constraint breach and suboptimal region by
 recreating local version of the problem around these regions. Each type of
@@ -168,4 +169,5 @@ constraint can be locally *reduced* and solved in its own way, to ensure fast
 .. code::
+
     pip install dnachisel     # <= minimal install without reports support
-    pip install dnachisel[reports] # <= full install with all dependencies
+    pip install 'dnachisel[reports]' # <= full install with all dependencies
 
@@ -175,3 +177,3 @@ The full installation using ``dnachisel[reports]`` downloads heavier libraries
 recommended to use DNA Chisel interactively via Python scripts. Also install
-[Geneblocks](https://edinburgh-genome-foundry.github.io/Geneblocks) and its
+`GeneBlocks <https://edinburgh-genome-foundry.github.io/Geneblocks>`_ and its
 dependencies if you wish to include a plot of sequence edits in the report.
@@ -196,3 +198,3 @@
 
-DnaChisel is an open-source software originally written at the `Edinburgh Genome Foundry
+DNA Chisel is an open-source software originally written at the `Edinburgh Genome Foundry
 <http://edinburgh-genome-foundry.github.io/home.html>`_ by `Zulko <https://github.com/Zulko>`_
@@ -199,0 +201,0 @@ and `released on Github <https://github.com/Edinburgh-Genome-Foundry/DnaChisel>`_ under the MIT licence (Copyright 2017 Edinburgh Genome Foundry). Everyone is welcome to contribute!

setup.py

@@ -49,4 +49,13 @@ # This will try to import setuptools. If not here, it will reach for the embedded
             "pandas",
-        ]
+        ],
+        "tests": [
+            "pytest",
+            "pytest-cov",
+            "coveralls",
+            "geneblocks",
+            "genome_collector",
+            "matplotlib",
+            "primer3-py",
+        ],
     },
 )

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