diff --git a/mutalyzer/describe.py b/mutalyzer/describe.py
index 38b8292473af23a86acb983e9b0fcc1883da99bf..44de257d0ab5d47fd1f01b2893e9cf76c89d5a13 100644
--- a/mutalyzer/describe.py
+++ b/mutalyzer/describe.py
@@ -9,6 +9,7 @@ leading from one sequence to an other.
from __future__ import unicode_literals
import collections
+
from Bio.SeqUtils import seq3
from Bio.Data import CodonTable
@@ -19,6 +20,18 @@ from mutalyzer import models
from extractor import extractor
+def printpos(s, start, end, fill=0):
+ """
+ For debugging purposes.
+ """
+ # TODO: See if this can partially replace or be merged with the
+ # visualisation in the __mutate() function of mutator.py
+ fs = 10 # Flank size.
+
+ return "{} {}{} {}".format(s[start - fs:start], s[start:end], '-' * fill,
+ s[end:end + fs])
+
+
def make_fs_tables(table_id):
"""
For every pair of amino acids, calculate the set of possible amino acids in
@@ -172,12 +185,10 @@ class Seq(object):
"""
Container for an inserted sequence.
"""
- #def __init__(self, sequence="", reference="", start=0, end=0,
def __init__(self, sequence="", start=0, end=0, reverse=False):
"""
"""
self.sequence = sequence
- #self.reference = reference
self.start = start
self.end = end
self.reverse = reverse
@@ -197,15 +208,6 @@ class Seq(object):
def __nonzero__(self):
return bool(self.sequence)
-
- #def dump(self):
- # """
- # Debug function.
- # """
- # if self.sequence:
- # return self.sequence
- # return self.reference[self.start:self.end]
- ##dump
#Seq
class SeqList(list):
@@ -216,21 +218,24 @@ class SeqList(list):
return "[{}]".format(representation)
return representation
#__str__
-
- #def __nonzero__(self):
- # return bool(len(self))
#SeqList
-class RawVar(models.RawVar):
+class HGVSVar(object):
+ def update(self):
+ self.hgvs = str(self)
+ self.hgvs_length = len(self)
+ #update
+#HGVSVar
+
+class DNAVar(models.DNAVar, HGVSVar):
"""
- Container for a raw variant.
+ Container for a DNA variant.
"""
- def __init__(self, dna=True, start=0, start_offset=0, end=0, end_offset=0,
+ def __init__(self, start=0, start_offset=0, end=0, end_offset=0,
sample_start=0, sample_start_offset=0, sample_end=0,
sample_end_offset=0, type="none", deleted=SeqList([Seq()]),
- inserted=SeqList([Seq()]), shift=0, start_aa="", end_aa="",
- term=0):
+ inserted=SeqList([Seq()]), shift=0):
"""
Initialise the class with the appropriate values.
@@ -261,7 +266,6 @@ class RawVar(models.RawVar):
"""
# TODO: Will this container be used for all variants, or only genomic?
# start_offset and end_offset may be never used.
- self.dna = dna
self.start = start
self.start_offset = start_offset
self.end = end
@@ -274,13 +278,10 @@ class RawVar(models.RawVar):
self.deleted = deleted
self.inserted = inserted
self.shift = shift
- self.start_aa = start_aa
- self.end_aa = end_aa
- self.term = term
self.update()
#__init__
- def _dna_description(self):
+ def __str__(self):
"""
Give the HGVS description of the raw variant stored in this class.
@@ -306,9 +307,83 @@ class RawVar(models.RawVar):
#if
return description + "{}>{}".format(self.deleted, self.inserted)
- #_dna_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
+ """
+ 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)
- def _protein_description(self):
+ 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):
+ """
+ Container for a raw variant.
+ """
+
+ def __init__(self, start=0, end=0, sample_start=0, sample_end=0,
+ type="none", deleted=SeqList([Seq()]), inserted=SeqList([Seq()]),
+ 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: str
+ :arg deleted: Deleted part of the reference sequence.
+ :type deleted: str
+ :arg inserted: Inserted part.
+ :type inserted: object
+ :arg shift: Amount of freedom.
+ :type shift: int
+ :arg term:
+ :type term:
+ """
+ self.start = start
+ self.end = end
+ self.sample_start = sample_start
+ self.sample_end = sample_end
+ self.type = type
+ self.deleted = deleted
+ self.inserted = inserted
+ self.shift = shift
+ self.term = term
+ self.update()
+ #__init__
+
+ def __str__(self):
"""
Give the HGVS description of the raw variant stored in this class.
@@ -345,40 +420,9 @@ class RawVar(models.RawVar):
if self.term:
return description + "fs*{}".format(self.term)
return description
- #_protein_description
-
- def _dna_description_length(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
- """
- 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.
- #_dna_description_length
+ #__str__
- def _protein_description_length(self):
+ def __len__(self):
"""
Give the standardised length of the HGVS description of the raw variant
stored in this class.
@@ -409,85 +453,41 @@ class RawVar(models.RawVar):
if self.term:
return description_length + len(self.type) + 2 # `*' + until stop.
return description_length
- #_protein_description_length
+ #__len__
+#ProteinVar
- def update(self):
- """
+class Allele(list):
+ def __str__(self):
"""
- self.hgvs = self.description()
- self.hgvs_length = self.description_length()
- #update
+ Convert a list of raw variants to an HGVS allele description.
- def description(self):
+ :returns: The HGVS description of {allele}.
+ :rtype: str
"""
- """
- if self.dna:
- return self._dna_description()
- return self._protein_description()
- #description
+ if len(self) > 1:
+ return "[{}]".format(';'.join(map(lambda x: x.hgvs, self)))
+ return self[0].hgvs
+ #__str__
- def description_length(self):
+ def length(self):
"""
- Give the standardised length of the HGVS description of the raw variant
- stored in this class.
+ Calculate the standardised length of an HGVS allele description.
- :returns: The standardised length of the HGVS description of the raw
- variant stored in this class.
+ :returns: The standardised length of the HGVS description of {allele}.
:rtype: int
"""
- if self.dna:
- return self._dna_description_length()
- return self._protein_description_length()
- #description_length
-#RawVar
-
-def allele_description(allele):
- """
- Convert a list of raw variants to an HGVS allele description.
+ # NOTE: Do we need to count the ; and [] ?
+ return sum(map(lambda x: x.hgvs_length, self))
+ #length
+#Allele
- :arg allele: A list of raw variants representing an allele description.
- :type allele: list(RawVar)
-
- :returns: The HGVS description of {allele}.
- :rtype: unicode
- """
- if len(allele) > 1:
- return "[{}]".format(';'.join(map(lambda x: x.hgvs, allele)))
- return allele[0].hgvs
-#allele_description
-
-def allele_description_length(allele):
- """
- Calculate the standardised length of an HGVS allele description.
-
- :arg allele: A list of raw variants representing an allele description.
- :type allele: list(RawVar)
-
- :returns: The standardised length of the HGVS description of {allele}.
- :rtype: int
- """
- # NOTE: Do we need to count the ; and [] ?
- return sum(map(lambda x: x.hgvs_length, allele))
-#allele_description_length
-
-def printpos(s, start, end, fill=0):
- """
- For debugging purposes.
- """
- # TODO: See if this can partially replace or be merged with the
- # visualisation in the __mutate() function of mutator.py
- fs = 10 # Flank size.
-
- return "{} {}{} {}".format(s[start - fs:start], s[start:end], '-' * fill,
- s[end:end + fs])
-#printpos
-def var_to_rawvar(s1, s2, var, seq_list=[], dna=True):
+def var_to_rawvar(s1, s2, var, seq_list=[], container=DNAVar):
"""
"""
# Unknown.
if s1 == '?' or s2 == '?':
- return [RawVar(dna=dna, type="unknown")]
+ return [container(type="unknown")]
# Insertion / Duplication.
if var.reference_start == var.reference_end:
@@ -500,17 +500,17 @@ def var_to_rawvar(s1, s2, var, seq_list=[], dna=True):
var.sample_start += shift3
var.sample_end += shift3
- if (var.sample_start - ins_length >= 0 and
+ if not seq_list and (var.sample_start - ins_length >= 0 and
s1[var.reference_start - ins_length:var.reference_start] ==
s2[var.sample_start:var.sample_end]):
- return RawVar(dna=dna, start=var.reference_start - ins_length + 1,
+ return container(start=var.reference_start - ins_length + 1,
end=var.reference_end, type="dup", shift=shift,
sample_start=var.sample_start + 1, sample_end=var.sample_end,
inserted=SeqList([Seq(sequence=s2[
var.sample_start:var.sample_end])]))
#if
- return RawVar(dna=dna, start=var.reference_start,
+ return container(start=var.reference_start,
end=var.reference_start + 1,
inserted=seq_list or
SeqList([Seq(sequence=s2[var.sample_start:var.sample_end])]),
@@ -526,7 +526,7 @@ def var_to_rawvar(s1, s2, var, seq_list=[], dna=True):
var.reference_start += shift3
var.reference_end += shift3
- return RawVar(dna=dna, start=var.reference_start + 1,
+ return container(start=var.reference_start + 1,
end=var.reference_end, type="del", shift=shift,
sample_start=var.sample_start, sample_end=var.sample_end + 1,
deleted=SeqList([Seq(sequence=s1[
@@ -537,7 +537,7 @@ def var_to_rawvar(s1, s2, var, seq_list=[], dna=True):
if (var.reference_start + 1 == var.reference_end and
var.sample_start + 1 == var.sample_end):
- return RawVar(dna=dna, start=var.reference_start + 1,
+ return container(start=var.reference_start + 1,
end=var.reference_end, sample_start=var.sample_start + 1,
sample_end=var.sample_end, type="subst",
deleted=SeqList([Seq(sequence=s1[var.reference_start])]),
@@ -553,7 +553,7 @@ def var_to_rawvar(s1, s2, var, seq_list=[], dna=True):
var.sample_end -= trim
#if
- return RawVar(dna=dna, start=var.reference_start + 1,
+ return container(start=var.reference_start + 1,
end=var.reference_end, type="inv",
sample_start=var.sample_start + 1, sample_end=var.sample_end,
deleted=SeqList([Seq(sequence=s1[
@@ -563,7 +563,7 @@ def var_to_rawvar(s1, s2, var, seq_list=[], dna=True):
#if
# InDel.
- return RawVar(dna=dna, start=var.reference_start + 1,
+ return container(start=var.reference_start + 1,
end=var.reference_end, deleted=SeqList([Seq(sequence=s1[
var.reference_start:var.reference_end])]), inserted=seq_list or
SeqList([Seq(sequence=s2[var.sample_start:var.sample_end])]),
@@ -583,7 +583,7 @@ def describe(s1, s2, dna=True):
:returns: A list of RawVar objects, representing the allele.
:rtype: list(RawVar)
"""
- description = []
+ description = Allele()
if not dna:
fs1, fs2 = make_fs_tables(1)
@@ -611,7 +611,7 @@ def describe(s1, s2, dna=True):
s2_part = s2
for variant in extractor.extract(unicode(s1_part), len(s1_part),
unicode(s2_part), len(s2_part), 1):
- description.append(var_to_rawvar(s1, s2, variant, dna=dna))
+ description.append(var_to_rawvar(s1, s2, variant, container=ProteinVar))
if description:
description[-1].term = term + 2
@@ -623,8 +623,8 @@ def describe(s1, s2, dna=True):
for variant in extractor.extract(unicode(s1), len(s1), unicode(s2), len(s2),
0):
- #print variant.type, variant.reference_start, variant.reference_end, variant.sample_start, variant.sample_end, variant.transposition_start, variant.transposition_end
- #print variant.type & extractor.TRANSPOSITION_OPEN, variant.type & extractor.TRANSPOSITION_CLOSE
+ print variant.type, variant.reference_start, variant.reference_end, variant.sample_start, variant.sample_end, variant.transposition_start, variant.transposition_end
+ print variant.type & extractor.TRANSPOSITION_OPEN, variant.type & extractor.TRANSPOSITION_CLOSE
if variant.type & extractor.TRANSPOSITION_OPEN:
if not in_transposition:
@@ -646,14 +646,13 @@ def describe(s1, s2, dna=True):
sequence=s2[variant.sample_start:variant.sample_end]))
#if
elif not (variant.type & extractor.IDENTITY):
- description.append(var_to_rawvar(s1, s2, variant, dna=dna))
+ description.append(var_to_rawvar(s1, s2, variant))
if variant.type & extractor.TRANSPOSITION_CLOSE:
in_transposition -= 1
if not in_transposition:
- description.append(var_to_rawvar(s1, s2, variant, seq_list,
- dna=dna))
+ description.append(var_to_rawvar(s1, s2, variant, seq_list))
#for i in seq_list:
# print i.dump()
#if
@@ -662,7 +661,7 @@ def describe(s1, s2, dna=True):
# Nothing happened.
if not description:
- return [RawVar(dna=dna)]
+ return Allele(RawVar())
return description
#describe
diff --git a/mutalyzer/entrypoints/mutalyzer.py b/mutalyzer/entrypoints/mutalyzer.py
index b499142c24dadb07a74bf85eeeb0fc0a9f59e7fc..f2a4b10de57f038cd2f6342b6067a1ecbbc4db69 100644
--- a/mutalyzer/entrypoints/mutalyzer.py
+++ b/mutalyzer/entrypoints/mutalyzer.py
@@ -111,9 +111,9 @@ def check_name(description):
extracted = extracted_protein = '(skipped)'
if extracted_allele:
- extracted = describe.allele_description(extracted_allele)
+ extracted = extracted_allele
if extracted_protein_allele:
- extracted_protein = describe.allele_description(extracted_protein_allele)
+ extracted_protein = extracted_protein_allele
print "\nExperimental services:"
print extracted
diff --git a/mutalyzer/models.py b/mutalyzer/models.py
index 10012a833aa8be71106d6c4941de443c3ccd434a..67d3d83a13661bb2cca2f7f47123bb37eee6f905 100644
--- a/mutalyzer/models.py
+++ b/mutalyzer/models.py
@@ -130,6 +130,56 @@ class RawVar(ComplexModel):
#RawVar
+class _RawVar(ComplexModel):
+ """
+ Used in MutalyzerOutput data type.
+ """
+ __namespace__ = SOAP_NAMESPACE
+
+ start = Mandatory.Integer
+ end = Mandatory.Integer
+ sample_start = Mandatory.Integer
+ sample_end = Mandatory.Integer
+ type = Mandatory.Unicode
+ deleted = Mandatory.Unicode
+ inserted = Mandatory.Unicode
+ shift = Mandatory.Integer
+ hgvs = Mandatory.Unicode
+ hgvs_length = Mandatory.Integer
+#_RawVar
+
+
+class DNAVar(_RawVar):
+ """
+ Used in MutalyzerOutput data type.
+ """
+ __namespace__ = SOAP_NAMESPACE
+
+ start_offset = Mandatory.Integer
+ end_offset = Mandatory.Integer
+ sample_start_offset = Mandatory.Integer
+ sample_end_offset = Mandatory.Integer
+#DNAVar
+
+
+class RNAVar(DNAVar):
+ """
+ Used in MutalyzerOutput data type.
+ """
+ __namespace__ = SOAP_NAMESPACE
+#RNAVar
+
+
+class ProteinVar(_RawVar):
+ """
+ Used in MutalyzerOutput data type.
+ """
+ __namespace__ = SOAP_NAMESPACE
+
+ term = Mandatory.Integer
+#ProteinVar
+
+
class Allele(ComplexModel):
"""
Used in MutalyzerOutput data type.