From d723e09e42eac7e9ce6201658728bf2c531c15de Mon Sep 17 00:00:00 2001
From: "J.F.J. Laros" <j.f.j.laros@lumc.nl>
Date: Fri, 1 Aug 2014 17:42:39 +0200
Subject: [PATCH] Removed the length and hgvs precalculation.
---
mutalyzer/describe.py | 98 ++----------------------------
mutalyzer/entrypoints/mutalyzer.py | 7 ++-
2 files changed, 10 insertions(+), 95 deletions(-)
diff --git a/mutalyzer/describe.py b/mutalyzer/describe.py
index c76ff4c4..b0b46842 100644
--- a/mutalyzer/describe.py
+++ b/mutalyzer/describe.py
@@ -218,15 +218,7 @@ class SeqList(list):
#__str__
#SeqList
-class HGVSVar(object):
- # NOTE: This may be obsolete, but check the JSON generation.
- def update(self):
- self.hgvs = str(self)
- self.hgvs_length = len(self)
- #update
-#HGVSVar
-
-class DNAVar(models.DNAVar, HGVSVar):
+class DNAVar(models.DNAVar):
"""
Container for a DNA variant.
"""
@@ -277,7 +269,6 @@ class DNAVar(models.DNAVar, HGVSVar):
self.deleted = deleted
self.inserted = inserted
self.shift = shift
- self.update()
#__init__
def __str__(self):
@@ -307,41 +298,9 @@ class DNAVar(models.DNAVar, HGVSVar):
return description + "{}>{}".format(self.deleted, self.inserted)
#__str__
-
- def __len__(self):
- """
- Give the standardised length of 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.
-
- :returns: The standardised length of the HGVS description of the raw
- variant stored in this class.
- :rtype: int
- """
- # NOTE: Obsolete?
- if self.type in ("none", "unknown"): # `=' or `?'
- return 1
-
- description_length = 1 # Start position.
-
- if self.start != self.end: # '_' and end position.
- description_length += 2
-
- if self.type != "subst":
- description_length += len(self.type)
-
- if self.type in ("ins", "delins"):
- return description_length + len(self.inserted)
- return description_length
- #if
-
- return 4 # Start position, '>' and end position.
- #__len__
#DNAVar
-class ProteinVar(models.ProteinVar, HGVSVar):
+class ProteinVar(models.ProteinVar):
"""
Container for a raw variant.
"""
@@ -380,7 +339,6 @@ class ProteinVar(models.ProteinVar, HGVSVar):
self.inserted = inserted
self.shift = shift
self.term = term
- self.update()
#__init__
def __str__(self):
@@ -421,40 +379,6 @@ class ProteinVar(models.ProteinVar, HGVSVar):
return description + "fs*{}".format(self.term)
return description
#__str__
-
- def __len__(self):
- """
- Give the standardised length of 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.
-
- :returns: The standardised length of the HGVS description of the raw
- variant stored in this class.
- :rtype: int
- """
- # NOTE: Obsolete?
- if not self.start: # =
- return 1
-
- description_length = 1 # Start position.
- if not self.deleted and self.type == "ext":
- description_length += 1 # *
- else:
- description_length += 3 # One amino acid.
- if self.end:
- description_length += 5 # `_' + one amino acid + end position.
- if self.type not in ["subst", "stop", "ext", "fs"]:
- description_length += len(self.type)
- if self.inserted:
- description_length += 3 * len(self.inserted)
- if self.type == "stop":
- return description_length + 1 # *
- if self.term:
- return description_length + len(self.type) + 2 # `*' + until stop.
- return description_length
- #__len__
#ProteinVar
class Allele(list):
@@ -466,21 +390,9 @@ class Allele(list):
:rtype: str
"""
if len(self) > 1:
- return "[{}]".format(';'.join(map(lambda x: x.hgvs, self)))
- return self[0].hgvs
+ return "[{}]".format(';'.join(map(lambda x: str(x), self)))
+ return str(self[0])
#__str__
-
- def length(self):
- """
- Calculate the standardised length of an HGVS allele description.
-
- :returns: The standardised length of the HGVS description of {allele}.
- :rtype: int
- """
- # NOTE: Do we need to count the ; and [] ?
- # NOTE: Obsolete?
- return sum(map(lambda x: x.hgvs_length, self))
- #length
#Allele
@@ -671,8 +583,6 @@ def describe_protein(s1, s2):
if description:
description[-1].term = term + 2
- description[-1].update()
- #if
return description
#describe_protein
diff --git a/mutalyzer/entrypoints/mutalyzer.py b/mutalyzer/entrypoints/mutalyzer.py
index dc1ea008..8110846e 100644
--- a/mutalyzer/entrypoints/mutalyzer.py
+++ b/mutalyzer/entrypoints/mutalyzer.py
@@ -18,7 +18,12 @@ from .. import variantchecker
class MyEncoder(json.JSONEncoder):
def default(self, o):
- return o.__dict__
+ json_object = o.__dict__
+ json_object.update({"hgvs": str(o)})
+
+ return json_object
+ #default
+#MyEncoder
def check_name(description):
"""
--
GitLab