Merge pull request #6

Add property setters and deleters

Author: Kronopt

.conda/fastaparser/meta.yaml

@@ -1,7 +1,7 @@
 # conda package recipe
 
 {% set name = "fastaparser" %}
-{% set version = "1.0" %}
+{% set version = "1.1" %}
 
 package:
   name: "{{ name|lower }}"
@@ -34,7 +34,7 @@ about:
   license: "GNU General Public v3 (GPLv3)"
   license_family: GPL3
   license_file: LICENSE
-  summary: "A Python FASTA file Parser and Writer"
+  summary: "A Python FASTA file Parser and Writer."
   doc_url: https://fastaparser.readthedocs.io/en/latest/
   dev_url: https://github.com/Kronopt/FastaParser
 

.github/ISSUE_TEMPLATE/bug_report.md

@@ -12,7 +12,8 @@ assignees: ''
 - Python version: 
 - Python interpreter: [Cpython (default), Jython, PyPy, etc]
 - Python packages installed: 
-- Install method: [pip, conda, other]
+- FastaParser install method: [pip, conda, other]
+- FastaParser version: 
 
 **Describe the bug**
 Describe the bug as precisely as possible.

.github/workflows/workflow.yml

@@ -1,8 +1,6 @@
 name: CI
 on: [push]
-
 jobs:
-  
   tests:
     runs-on: ubuntu-latest
     strategy:

docs/api_fastasequence.md

@@ -25,12 +25,18 @@ Instances of the FastaSequence class have the following attributes
 
 | Attribute | Type / Value | Editable | Description |
 |:---:|:---:|:---:|---|
-| id | str | No | ID portion of the definition line (header). Can be empty |
-| description | str | No | Description portion of the definition line (header). Can be empty |
+| id | str | Yes | ID portion of the definition line (header). Can be empty |
+| description | str | Yes | Description portion of the definition line (header). Can be empty |
 | sequence | list([LetterCode](api_lettercode.md)) | No | Sequence |
 | sequence_type | 'nucleotide', 'aminoacid' or None | Yes | Indicates the sequence type. Can be `None` if not known |
 | inferred_type | bool | No | `True` if `FastaSequence` inferred the sequence type, `False` otherwise.
 
+Editable attributes can be set by standard variable assignment and deleted/reset with the del keyword:
+```Python
+fastasequence_object.id = 'new_id'
+del fastasequence_object.description
+```
+
 ## Methods
 Instances of the FastaSequence class have the following methods
 

docs/api_lettercode.md

@@ -29,6 +29,12 @@ Instances of the LetterCode class have the following attributes
 | supported | bool | No | Indicates if letter code is supported or not (ie, if `letter_type` is provided and letter code is defined in the FASTA specification). |
 | in_fasta_spec | bool | No | Indicates if letter code is defined in the FASTA specification. |
 
+Editable attributes can be set by standard variable assignment and deleted/reset with the del keyword:
+```Python
+lettercode_object.letter_type = 'nucleotide'
+del lettercode_object.letter_type
+```
+
 ## Methods
 Instances of the LetterCode class have the following method
 

docs/history.md

@@ -1,5 +1,15 @@
 # History
 
+### 1.1 (13-02-2020)
+* Added property setters for:
+    * FastaSequence.id
+    * FastaSequence.description
+* Added property deleters for:
+    * FastaSequence.id
+    * FastaSequence.description
+    * FastaSequence.sequence_type
+    * LetterCode.letter_type
+
 ### 1.0 (27-01-2020)
 * First release on PyPI and Anaconda Cloud
 * Reader, Writer, FastaSequence and LetterCode classes

fastaparser/__init__.py

@@ -32,7 +32,7 @@
 
 __author__ = 'Pedro HC David, https://github.com/Kronopt'
 __credits__ = ['Pedro HC David']
-__version__ = '1.0'
+__version__ = '1.1'
 __license__ = 'GPLv3'
 
 

fastaparser/fastasequence.py

@@ -61,6 +61,8 @@ class FastaSequence:
     TypeError
         When calling __init__, if sequence, id_, description, sequence_type or infer_type are of the wrong type.
         When calling from_fastasequence(), if fastasequence is of the wrong type.
+        When setting id, if id_value is not str.
+        When setting description, if description_value is not str.
         When setting sequence_type, if sequence_type_value is of the wrong type.
         When calling complement(), if sequence_type is 'aminoacid' or reverse is not bool.
         When calling gc_content(), if sequence_type is 'aminoacid' or as_percentage is not bool.
@@ -99,19 +101,8 @@ def __init__(self, sequence, id_='', description='', sequence_type=None, infer_t
         TypeError
             If sequence, id_, description, sequence_type or infer_type are of the wrong type.
         """
-        if isinstance(id_, str):
-            id_ = ''.join(id_.strip().replace(' ', '_').split())  # remove spaces and newlines
-            if id_.startswith('>'):  # remove '>' if any
-                id_ = id_[1:]
-            self._id = id_
-        else:
-            raise TypeError('id_ must be str')
-
-        if isinstance(description, str):
-            self._description = ' '.join(description.strip().split())  # remove extra spaces and newlines
-        else:
-            raise TypeError('description must be str')
-
+        self._update_id(id_)
+        self._update_description(description)
         self._update_sequence_type(sequence_type, update_letter_code_objects=False)
 
         if isinstance(sequence, str) and len(sequence) > 0:
@@ -165,11 +156,63 @@ def id(self):
         """return id."""
         return self._id
 
+    @id.setter
+    def id(self, id_value):
+        """
+        Sets id.
+        '>' and newlines will be removed, if any. Spaces will be converted to '_'.
+        Can be an empty string.
+
+        Parameters
+        ----------
+        id_value : str
+            ID portion of the definition line (header).
+
+        Raises
+        ------
+        TypeError
+            If id_value is not str.
+        """
+        self._update_id(id_value)
+
+    @id.deleter
+    def id(self):
+        """
+        Sets id to the default value ('').
+        """
+        self._update_id('')
+
     @property
     def description(self):
         """return description."""
         return self._description
 
+    @description.setter
+    def description(self, description_value):
+        """
+        Sets description.
+        Newlines will be removed, if any.
+        Can be an empty string.
+
+        Parameters
+        ----------
+        description_value : str
+            Description portion of the definition line (header).
+
+        Raises
+        ------
+        TypeError
+            If description_value is not str.
+        """
+        self._update_description(description_value)
+
+    @description.deleter
+    def description(self):
+        """
+        Sets description to the default value ('').
+        """
+        self._update_description('')
+
     @property
     def sequence(self):
         """return sequence."""
@@ -197,6 +240,13 @@ def sequence_type(self, sequence_type_value):
         """
         self._update_sequence_type(sequence_type_value)
 
+    @sequence_type.deleter
+    def sequence_type(self):
+        """
+        Sets sequence_type to the default value (None) and updates all other relevant properties as needed.
+        """
+        self._update_sequence_type(None)
+
     @property
     def inferred_type(self):
         """return inferred_type."""
@@ -374,7 +424,7 @@ def count_letter_codes_degenerate(self):
             return {letter: counts for letter, counts in self._counts.items()
                     if letter in LETTER_CODES[self._sequence_type][1]}
         raise TypeError('To count degenerate letter codes the sequence_type must be '
-                        'explicitly \'%s\'' % ('\' or \''.join(LETTER_CODES),))
+                        'explicitly \'%s\'' % '\' or \''.join(LETTER_CODES))
 
     def formatted_definition_line(self):
         """
@@ -457,6 +507,51 @@ def reverse(self):
         """
         return self.__reversed__()
 
+    def _update_id(self, id_):
+        """
+        Updates ID portion of the definition line (header).
+        '>' and newlines will be removed, if any. Spaces will be converted to '_'.
+        Can be an empty string.
+
+        Parameters
+        ----------
+        id_ : str
+            ID portion of the definition line (header).
+
+        Raises
+        ------
+        TypeError
+            If id_ is not str.
+        """
+        if isinstance(id_, str):
+            id_ = ''.join(id_.strip().replace(' ', '_').split())  # remove spaces and newlines
+            if id_.startswith('>'):  # remove '>' if any
+                id_ = id_[1:]
+            self._id = id_
+        else:
+            raise TypeError('id_ must be str')
+
+    def _update_description(self, description):
+        """
+        Updates description portion of the definition line (header).
+        Newlines will be removed, if any.
+        Can be an empty string.
+
+        Parameters
+        ----------
+        description : str
+            Description portion of the definition line (header).
+
+        Raises
+        ------
+        TypeError
+            If description is not str.
+        """
+        if isinstance(description, str):
+            self._description = ' '.join(description.strip().split())  # remove extra spaces and newlines
+        else:
+            raise TypeError('description must be str')
+
     def _update_sequence_type(self, sequence_type, update_letter_code_objects=True):
         """
         Updates sequence_type and all other relevant properties as needed.
@@ -477,7 +572,7 @@ def _update_sequence_type(self, sequence_type, update_letter_code_objects=True):
             self._sequence_type = sequence_type
             self._inferred_type = False
         else:
-            raise TypeError('sequence_type must be one of: %s or None' % LETTER_CODES)
+            raise TypeError('sequence_type must be one of: \'%s\' or None' % '\', \''.join(LETTER_CODES))
         if isinstance(update_letter_code_objects, bool):
             if update_letter_code_objects:
                 for letter_code_object in self._sequence:  # update LetterCode objects

fastaparser/lettercode.py

@@ -124,6 +124,13 @@ def letter_type(self, letter_type_value):
         """
         self._update_letter_type(letter_type_value)
 
+    @letter_type.deleter
+    def letter_type(self):
+        """
+        Sets letter_type to the default value (None) and updates all other relevant properties as needed.
+        """
+        self._update_letter_type(None)
+
     @property
     def description(self):
         """return description."""