From 753bf60059a6cea43275c1865288310f06759f8c Mon Sep 17 00:00:00 2001
From: "Jeroen F.J. Laros" <jlaros@fixedpoint.nl>
Date: Sun, 19 Apr 2015 14:32:02 +0200
Subject: [PATCH] Updated documentation.
---
mutalyzer/describe.py | 27 +++++++------
mutalyzer/variant.py | 92 +++++++++++++++++--------------------------
2 files changed, 51 insertions(+), 68 deletions(-)
diff --git a/mutalyzer/describe.py b/mutalyzer/describe.py
index c4f1da77..f17114ef 100644
--- a/mutalyzer/describe.py
+++ b/mutalyzer/describe.py
@@ -31,6 +31,15 @@ def printpos(s, start, end, fill=0):
def var_to_rawvar(s1, s2, var, seq_list=[], container=DNAVar,
weight_position=1):
"""
+ Convert a variant from the extractor module to one of the RawVar
+ subclasses.
+
+ :arg unicode s1: Reference sequence.
+ :arg unicode s2: Sample sequence.
+ :arg str var: Variant from the extractor module.
+ :arg str seq_list: Container for an inserted sequence.
+ :arg str container: Destination container.
+ :arg str weight_position: Weight of a position.
"""
# Unknown.
if s1 == '?' or s2 == '?':
@@ -131,13 +140,10 @@ def describe_dna(s1, s2):
"""
Give an allele description of the change from {s1} to {s2}.
- :arg s1: Sequence 1.
- :type s1: unicode
- :arg s2: Sequence 2.
- :type s2: unicode
+ :arg unicode s1: Sequence 1.
+ :arg unicode s2: Sequence 2.
- :returns: A list of RawVar objects, representing the allele.
- :rtype: list(RawVar)
+ :returns list(RawVar): A list of RawVar objects, representing the allele.
"""
description = Allele()
in_transposition = 0
@@ -190,13 +196,10 @@ def describe_protein(s1, s2):
"""
Give an allele description of the change from {s1} to {s2}.
- :arg s1: Sequence 1.
- :type s1: unicode
- :arg s2: Sequence 2.
- :type s2: unicode
+ :arg unicode s1: Sequence 1.
+ :arg unicode s2: Sequence 2.
- :returns: A list of RawVar objects, representing the allele.
- :rtype: list(RawVar)
+ :returns list(RawVar): A list of RawVar objects, representing the allele.
"""
description = Allele()
diff --git a/mutalyzer/variant.py b/mutalyzer/variant.py
index fc3818d3..2ea2d393 100644
--- a/mutalyzer/variant.py
+++ b/mutalyzer/variant.py
@@ -1,4 +1,5 @@
"""
+Models for the description extractor.
"""
from __future__ import unicode_literals
@@ -71,14 +72,12 @@ class ISeq(object):
def __init__(self, sequence='', start=0, end=0, reverse=False,
weight_position=1):
"""
- :arg sequence: Literal inserted sequence.
- :type sequence: unicode
- :arg start: Start position for a transposed sequence.
- :type start: int
- :arg end: End position for a transposed sequence.
- :type end: int
- :arg reverse: Inverted transposed sequence.
- :type reverse: bool
+ Initialise the class with the appropriate values.
+
+ :arg unicode sequence: Literal inserted sequence.
+ :arg int start: Start position for a transposed sequence.
+ :arg int end: End position for a transposed sequence.
+ :arg bool reverse: Inverted transposed sequence.
"""
self.sequence = sequence
self.start = start
@@ -130,30 +129,18 @@ class DNAVar(object):
"""
Initialise the class with the appropriate values.
- :arg start: Start position.
- :type start: int
- :arg start_offset:
- :type start_offset: int
- :arg end: End position.
- :type end: int
- :arg end_offset:
- :type end_offset: int
- :arg sample_start: Start position.
- :type sample_start: int
- :arg sample_start_offset:
- :type sample_start_offset: int
- :arg sample_end: End position.
- :type sample_end: int
- :arg sample_end_offset:
- :type sample_end_offset: int
- :arg type: Variant type.
- :type type: unicode
- :arg deleted: Deleted part of the reference sequence.
- :type deleted: unicode
- :arg inserted: Inserted part.
- :type inserted: object
- :arg shift: Amount of freedom.
- :type shift: int
+ :arg int start: Start position.
+ :arg int start_offset:
+ :arg int end: End position.
+ :arg int end_offset:
+ :arg int sample_start: Start position.
+ :arg int sample_start_offset:
+ :arg int sample_end: End position.
+ :arg int sample_end_offset:
+ :arg unicode type: Variant type.
+ :arg unicode deleted: Deleted part of the reference sequence.
+ :arg ISeqList inserted: Inserted part.
+ :arg int shift: Amount of freedom.
"""
# TODO: Will this container be used for all variants, or only genomic?
# start_offset and end_offset may be never used.
@@ -176,8 +163,8 @@ class DNAVar(object):
"""
Give the HGVS description of the raw variant stored in this class.
- :returns: The HGVS description of the raw variant stored in this class.
- :rtype: unicode
+ :returns unicode: The HGVS description of the raw variant stored in
+ this class.
"""
if self.type == 'unknown':
return '?'
@@ -215,31 +202,24 @@ class DNAVar(object):
class ProteinVar(object):
"""
Container for a protein variant.
+
"""
+ #NOTE: This is experimental code. It is not used at the moment.
def __init__(self, start=0, end=0, sample_start=0, sample_end=0,
type='none', deleted=ISeqList([ISeq()]),
inserted=ISeqList([ISeq()]), shift=0, term=0):
"""
Initialise the class with the appropriate values.
- :arg start: Start position.
- :type start: int
- :arg end: End position.
- :type end: int
- :arg sample_start: Start position.
- :type sample_start: int
- :arg sample_end: End position.
- :type sample_end: int
- :arg type: Variant type.
- :type type: unicode
- :arg deleted: Deleted part of the reference sequence.
- :type deleted: unicode
- :arg inserted: Inserted part.
- :type inserted: object
- :arg shift: Amount of freedom.
- :type shift: int
- :arg term:
- :type term:
+ :arg int start: Start position.
+ :arg int end: End position.
+ :arg int sample_start: Start position.
+ :arg int sample_end: End position.
+ :arg unicode type: Variant type.
+ :arg unicode deleted: Deleted part of the reference sequence.
+ :arg ISeqList inserted: Inserted part.
+ :arg int shift: Amount of freedom.
+ :arg int term: Number of positions until stop codon.
"""
self.start = start
self.end = end
@@ -257,10 +237,10 @@ class ProteinVar(object):
Give the HGVS description of the raw variant stored in this class.
Note that this function relies on the absence of values to make the
- correct description. Also see the comment in the class definition.
+ correct description. The method used in the DNAVar is better.
- :returns: The HGVS description of the raw variant stored in this class.
- :rtype: unicode
+ :returns unicode: The HGVS description of the raw variant stored in
+ this class.
"""
if self.type == 'unknown':
return '?'
@@ -278,7 +258,7 @@ class ProteinVar(object):
description += '{}'.format(self.start)
if self.end:
description += '_{}{}'.format(seq3(self.end_aa), self.end)
- if self.type not in ['subst', 'stop', 'ext', 'fs']: # fs is not a type
+ if self.type not in ('subst', 'stop', 'ext', 'fs'): # fs is not a type
description += self.type
if self.inserted:
description += '{}'.format(seq3(self.inserted))
--
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