diff --git a/mutalyzer/describe.py b/mutalyzer/describe.py
index 1b8b658e2b39a631e5d8df006e32112fc2a5a709..d702999ae21ca0c7ec3796541416f5365e8ba641 100644
--- a/mutalyzer/describe.py
+++ b/mutalyzer/describe.py
@@ -19,7 +19,7 @@ from mutalyzer import models
from extractor import extractor
-def makeFSTables(table_id):
+def make_fs_tables(table_id):
"""
For every pair of amino acids, calculate the set of possible amino acids in
a different reading frame. Do this for both alternative reading frames (+1
@@ -41,19 +41,19 @@ def makeFSTables(table_id):
reverse_table[table[i]].append(i)
# Make the frame shift tables.
- FS1 = collections.defaultdict(set)
- FS2 = collections.defaultdict(set)
- for AA_i in reverse_table:
- for AA_j in reverse_table:
- for codon_i in reverse_table[AA_i]:
- for codon_j in reverse_table[AA_j]:
- FS1[AA_i + AA_j].add(table[(codon_i + codon_j)[1:4]]) # +1.
- FS2[AA_i + AA_j].add(table[(codon_i + codon_j)[2:5]]) # +2.
+ fs1 = collections.defaultdict(set)
+ fs2 = collections.defaultdict(set)
+ for aa_i in reverse_table:
+ for aa_j in reverse_table:
+ for codon_i in reverse_table[aa_i]:
+ for codon_j in reverse_table[aa_j]:
+ fs1[aa_i + aa_j].add(table[(codon_i + codon_j)[1:4]]) # +1.
+ fs2[aa_i + aa_j].add(table[(codon_i + codon_j)[2:5]]) # +2.
#for
- return FS1, FS2
-#makeFSTables
+ return fs1, fs2
+#make_fs_tables
-def __makeOverlaps(peptide):
+def _peptide_overlaps(peptide):
"""
Make a list of overlapping 2-mers of {peptide} in order of appearance.
@@ -63,102 +63,102 @@ def __makeOverlaps(peptide):
@rtype: list(unicode)
"""
return map(lambda x: peptide[x:x+2], range(len(peptide) - 1))
-#__makeOverlaps
+#_peptide_overlaps
-def __options(pList, peptidePrefix, FS, output):
+def _options(peptide_overlaps, peptide_prefix, fs, output):
"""
Enumerate all peptides that could result from a frame shift.
- @arg pList: List of overlapping 2-mers of a peptide.
- @type pList: list(unicode)
- @arg peptidePrefix: Prefix of a peptide in the alternative reading frame.
- @type peptidePrefix: unicode
- @arg FS: Frame shift table.
- @type FS: dict
+ @arg peptide_overlaps: List of overlapping 2-mers of a peptide.
+ @type peptide_overlaps: list(unicode)
+ @arg peptide_prefix: Prefix of a peptide in the alternative reading frame.
+ @type peptide_prefix: unicode
+ @arg fs: Frame shift table.
+ @type fs: dict
@arg output: List of peptides, should be empty initially.
@type output: list(unicode)
"""
- if not pList:
- output.append(peptidePrefix)
+ if not peptide_overlaps:
+ output.append(peptide_prefix)
return
#if
- for i in FS[pList[0]]:
- __options(pList[1:], peptidePrefix + i, FS, output)
-#__options
+ for i in fs[peptide_overlaps[0]]:
+ _options(peptide_overlaps[1:], peptide_prefix + i, fs, output)
+#_options
-def enumFS(peptide, FS):
+def enum_fs(peptide, fs):
"""
Enumerate all peptides that could result from a frame shift.
@arg peptide: Original peptide sequence.
@type peptide: unicode
- @arg FS: Frame shift table.
- @type FS: dict
+ @arg fs: Frame shift table.
+ @type fs: dict
"""
output = []
- __options(__makeOverlaps(peptide), "", FS, output)
+ _options(_peptide_overlaps(peptide), "", fs, output)
return output
-#enumFS
+#enum_fs
-def fitFS(peptide, altPeptide, FS):
+def fit_fs(peptide, alternative_peptide, fs):
"""
- Check whether peptide {altPeptide} is a possible frame shift of peptide
- {peptide}.
+ Check whether peptide {alternative_peptide} is a possible frame shift of
+ peptide {peptide}.
@arg peptide: Original peptide sequence.
@type peptide: unicode
- @arg altPeptide: Observed peptide sequence.
- @type altPeptide: unicode
- @arg FS: Frame shift table.
- @type FS: dict
+ @arg alternative_peptide: Observed peptide sequence.
+ @type alternative_peptide: unicode
+ @arg fs: Frame shift table.
+ @type fs: dict
"""
# Todo: This is a temporary fix to prevent crashing on frameshift
# detection (I think bug #124).
return False
- if len(peptide) < len(altPeptide):
+ if len(peptide) < len(alternative_peptide):
return False
- pList = __makeOverlaps(peptide)
+ peptide_overlaps = _peptide_overlaps(peptide)
- for i in range(len(altPeptide)):
- if not altPeptide[i] in FS[pList[i]]:
+ for i in range(len(alternative_peptide)):
+ if not alternative_peptide[i] in fs[peptide_overlaps[i]]:
return False
return True
-#fitFS
+#fit_fs
-def findFS(peptide, altPeptide, FS):
+def find_fs(peptide, alternative_peptide, fs):
"""
- Find the longest part of {altPeptide} that fits in {peptide} in a certain
- frame given by {FS}.
+ Find the longest part of {alternative_peptide} that fits in {peptide} in a
+ certain frame given by {fs}.
@arg peptide: Original peptide sequence.
@type peptide: unicode
- @arg altPeptide: Observed peptide sequence.
- @type altPeptide: unicode
- @arg FS: Frame shift table.
- @type FS: dict
+ @arg alternative_peptide: Observed peptide sequence.
+ @type alternative_peptide: unicode
+ @arg fs: Frame shift table.
+ @type fs: dict
@returns: The length and the offset in {peptide} of the largest frameshift.
@rtype: tuple(int, int)
"""
- pList = __makeOverlaps(peptide)
- maxFS = 0
- fsStart = 0
+ peptide_overlaps = _peptide_overlaps(peptide)
+ max_fs = 0
+ fs_start = 0
- for i in range(len(pList))[::-1]:
- for j in range(min(i + 1, len(altPeptide))):
- if not altPeptide[::-1][j] in FS[pList[i - j]]:
+ for i in range(len(peptide_overlaps))[::-1]:
+ for j in range(min(i + 1, len(alternative_peptide))):
+ if not alternative_peptide[::-1][j] in fs[peptide_overlaps[i - j]]:
break
- if j >= maxFS:
- maxFS = j
- fsStart = i - j + 2
+ if j >= max_fs:
+ max_fs = j
+ fs_start = i - j + 2
#if
#for
- return maxFS - 1, fsStart
-#findFS
+ return max_fs - 1, fs_start
+#find_fs
class Seq(object):
"""
@@ -218,10 +218,11 @@ class RawVar(models.RawVar):
Container for a raw variant.
"""
- def __init__(self, DNA=True, start=0, start_offset=0, end=0, end_offset=0,
+ def __init__(self, dna=True, 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, startAA="", endAA="", term=0):
+ inserted=SeqList([Seq()]), shift=0, start_aa="", end_aa="",
+ term=0):
"""
Initialise the class with the appropriate values.
@@ -252,7 +253,7 @@ 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.dna = dna
self.start = start
self.start_offset = start_offset
self.end = end
@@ -265,15 +266,13 @@ class RawVar(models.RawVar):
self.deleted = deleted
self.inserted = inserted
self.shift = shift
- self.startAA = startAA
- self.endAA = endAA
+ self.start_aa = start_aa
+ self.end_aa = end_aa
self.term = term
self.update()
- #self.hgvs = self.description()
- #self.hgvsLength = self.descriptionLength()
#__init__
- def __DNADescription(self):
+ def _dna_description(self):
"""
Give the HGVS description of the raw variant stored in this class.
@@ -283,23 +282,23 @@ class RawVar(models.RawVar):
if not self.start:
return "="
- descr = "{}".format(self.start)
+ description = "{}".format(self.start)
if self.start != self.end:
- descr += "_{}".format(self.end)
+ description += "_{}".format(self.end)
if self.type != "subst":
- descr += "{}".format(self.type)
+ description += "{}".format(self.type)
if self.type in ("ins", "delins"):
- return descr + "{}".format(self.inserted)
- return descr
+ return description + "{}".format(self.inserted)
+ return description
#if
- return descr + "{}>{}".format(self.deleted, self.inserted)
- #__DNADescription
+ return description + "{}>{}".format(self.deleted, self.inserted)
+ #_dna_description
- def __proteinDescription(self):
+ def _protein_description(self):
"""
Give the HGVS description of the raw variant stored in this class.
@@ -314,31 +313,31 @@ class RawVar(models.RawVar):
if not self.start:
return "="
- descr = ""
+ description = ""
if not self.deleted:
if self.type == "ext":
- descr += '*'
+ description += '*'
else:
- descr += "{}".format(seq3(self.startAA))
+ description += "{}".format(seq3(self.start_aa))
#if
else:
- descr += "{}".format(seq3(self.deleted))
- descr += "{}".format(self.start)
+ description += "{}".format(seq3(self.deleted))
+ description += "{}".format(self.start)
if self.end:
- descr += "_{}{}".format(seq3(self.endAA), self.end)
+ description += "_{}{}".format(seq3(self.end_aa), self.end)
if self.type not in ["subst", "stop", "ext", "fs"]: # fs is not a type
- descr += self.type
+ description += self.type
if self.inserted:
- descr += "{}".format(seq3(self.inserted))
+ description += "{}".format(seq3(self.inserted))
if self.type == "stop":
- return descr + '*'
+ return description + '*'
if self.term:
- return descr + "fs*{}".format(self.term)
- return descr
- #__proteinDescription
+ return description + "fs*{}".format(self.term)
+ return description
+ #_protein_description
- def __DNADescriptionLength(self):
+ def _dna_description_length(self):
"""
Give the standardised length of the HGVS description of the raw variant
stored in this class.
@@ -353,23 +352,23 @@ class RawVar(models.RawVar):
if not self.start: # `=' or `?'
return 1
- descrLen = 1 # Start position.
+ description_length = 1 # Start position.
if self.end: # '_' and end position.
- descrLen += 2
+ description_length += 2
if self.type != "subst":
- descrLen += len(self.type)
+ description_length += len(self.type)
if self.inserted:
- return descrLen + len(self.inserted)
- return descrLen
+ return description_length + len(self.inserted)
+ return description_length
#if
return 4 # Start position, '>' and end position.
- #__DNAdescriptionLength
+ #_dna_description_length
- def __proteinDescriptionLength(self):
+ def _protein_description_length(self):
"""
Give the standardised length of the HGVS description of the raw variant
stored in this class.
@@ -384,40 +383,40 @@ class RawVar(models.RawVar):
if not self.start: # =
return 1
- descrLen = 1 # Start position.
+ description_length = 1 # Start position.
if not self.deleted and self.type == "ext":
- descrLen += 1 # *
+ description_length += 1 # *
else:
- descrLen += 3 # One amino acid.
+ description_length += 3 # One amino acid.
if self.end:
- descrLen += 5 # `_' + one amino acid + end position.
+ description_length += 5 # `_' + one amino acid + end position.
if self.type not in ["subst", "stop", "ext", "fs"]:
- descrLen += len(self.type)
+ description_length += len(self.type)
if self.inserted:
- descrLen += 3 * len(self.inserted)
+ description_length += 3 * len(self.inserted)
if self.type == "stop":
- return descrLen + 1 # *
+ return description_length + 1 # *
if self.term:
- return descrLen + len(self.type) + 2 # `*' + length until stop.
- return descrLen
- #__proteinDescriptionLength
+ return description_length + len(self.type) + 2 # `*' + until stop.
+ return description_length
+ #_protein_description_length
def update(self):
"""
"""
self.hgvs = self.description()
- self.hgvsLength = self.descriptionLength()
+ self.hgvs_length = self.description_length()
#update
def description(self):
"""
"""
- if self.DNA:
- return self.__DNADescription()
- return self.__proteinDescription()
+ if self.dna:
+ return self._dna_description()
+ return self._protein_description()
#description
- def descriptionLength(self):
+ def description_length(self):
"""
Give the standardised length of the HGVS description of the raw variant
stored in this class.
@@ -426,11 +425,11 @@ class RawVar(models.RawVar):
variant stored in this class.
@rtype: int
"""
- if self.DNA:
- return self.__DNADescriptionLength()
- return self.__proteinDescriptionLength()
- #descriptionLength
-#DescribeRawVar
+ if self.dna:
+ return self._dna_description_length()
+ return self._protein_description_length()
+ #description_length
+#RawVar
def allele_description(allele):
"""
@@ -447,7 +446,7 @@ def allele_description(allele):
return allele[0].hgvs
#allele_description
-def alleleDescriptionLength(allele):
+def allele_description_length(allele):
"""
Calculate the standardised length of an HGVS allele description.
@@ -458,8 +457,8 @@ def alleleDescriptionLength(allele):
@rval: int
"""
# NOTE: Do we need to count the ; and [] ?
- return sum(map(lambda x: x.hgvsLength, allele))
-#alleleDescriptionLength
+ return sum(map(lambda x: x.hgvs_length, allele))
+#allele_description_length
def printpos(s, start, end, fill=0):
"""
@@ -473,12 +472,12 @@ def printpos(s, start, end, fill=0):
s[end:end + fs])
#printpos
-def var2RawVar(s1, s2, var, seq_list=[], DNA=True):
+def var_to_rawvar(s1, s2, var, seq_list=[], dna=True):
"""
"""
# Unknown.
if s1 == '?' or s2 == '?':
- return [RawVar(DNA=DNA, type="unknown")]
+ return [RawVar(dna=dna, type="unknown")]
# Insertion / Duplication.
if var.reference_start == var.reference_end:
@@ -495,13 +494,13 @@ def var2RawVar(s1, s2, var, seq_list=[], DNA=True):
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 RawVar(dna=dna, 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 RawVar(dna=dna, start=var.reference_start,
end=var.reference_start + 1,
inserted=seq_list or
SeqList([Seq(sequence=s2[var.sample_start:var.sample_end])]),
@@ -517,7 +516,7 @@ def var2RawVar(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 RawVar(dna=dna, 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[
@@ -528,7 +527,7 @@ def var2RawVar(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 RawVar(dna=dna, 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])]),
@@ -544,7 +543,7 @@ def var2RawVar(s1, s2, var, seq_list=[], DNA=True):
var.sample_end -= trim
#if
- return RawVar(DNA=DNA, start=var.reference_start + 1,
+ return RawVar(dna=dna, 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[
@@ -554,15 +553,15 @@ def var2RawVar(s1, s2, var, seq_list=[], DNA=True):
#if
# InDel.
- return RawVar(DNA=DNA, start=var.reference_start + 1,
+ return RawVar(dna=dna, 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])]),
type="delins", sample_start=var.sample_start + 1,
sample_end=var.sample_end)
-#var2RawVar
+#var_to_rawvar
-def describe(s1, s2, DNA=True):
+def describe(s1, s2, dna=True):
"""
Give an allele description of the change from {s1} to {s2}.
@@ -576,31 +575,33 @@ def describe(s1, s2, DNA=True):
"""
description = []
- if not DNA:
- FS1, FS2 = makeFSTables(1)
- longestFSf = max(findFS(s1, s2, FS1), findFS(s1, s2, FS2))
- longestFSr = max(findFS(s2, s1, FS1), findFS(s2, s1, FS2))
-
- if longestFSf > longestFSr:
- print s1[:longestFSf[1]], s1[longestFSf[1]:]
- print s2[:len(s2) - longestFSf[0]], s2[len(s2) - longestFSf[0]:]
- s1_part = s1[:longestFSf[1]]
- s2_part = s2[:len(s2) - longestFSf[0]]
- term = longestFSf[0]
+ if not dna:
+ fs1, fs2 = make_fs_tables(1)
+ longest_fs_f = max(find_fs(s1, s2, fs1), find_fs(s1, s2, fs2))
+ longest_fs_r = max(find_fs(s2, s1, fs1), find_fs(s2, s1, fs2))
+
+ if longest_fs_f > longest_fs_r:
+ print s1[:longest_fs_f[1]], s1[longest_fs_f[1]:]
+ print s2[:len(s2) - longest_fs_f[0]], \
+ s2[len(s2) - longest_fs_f[0]:]
+ s1_part = s1[:longest_fs_f[1]]
+ s2_part = s2[:len(s2) - longest_fs_f[0]]
+ term = longest_fs_f[0]
#if
else:
- print s1[:len(s1) - longestFSr[0]], s1[len(s1) - longestFSr[0]:]
- print s2[:longestFSr[1]], s2[longestFSr[1]:]
- s1_part = s1[:len(s1) - longestFSr[0]]
- s2_part = s2[:longestFSr[1]]
- term = len(s2) - longestFSr[1]
+ print s1[:len(s1) - longest_fs_r[0]], \
+ s1[len(s1) - longest_fs_r[0]:]
+ print s2[:longest_fs_r[1]], s2[longest_fs_r[1]:]
+ s1_part = s1[:len(s1) - longest_fs_r[0]]
+ s2_part = s2[:longest_fs_r[1]]
+ term = len(s2) - longest_fs_r[1]
#else
s1_part = s1
s2_part = s2
for variant in extractor.extract(unicode(s1_part), len(s1_part),
unicode(s2_part), len(s2_part), 1):
- description.append(var2RawVar(s1, s2, variant, DNA=DNA))
+ description.append(var_to_rawvar(s1, s2, variant, dna=dna))
if description:
description[-1].term = term + 2
@@ -635,14 +636,14 @@ def describe(s1, s2, DNA=True):
sequence=s2[variant.sample_start:variant.sample_end]))
#if
elif not (variant.type & extractor.IDENTITY):
- description.append(var2RawVar(s1, s2, variant, DNA=DNA))
+ description.append(var_to_rawvar(s1, s2, variant, dna=dna))
if variant.type & extractor.TRANSPOSITION_CLOSE:
in_transposition -= 1
if not in_transposition:
- description.append(var2RawVar(s1, s2, variant, seq_list,
- DNA=DNA))
+ description.append(var_to_rawvar(s1, s2, variant, seq_list,
+ dna=dna))
#for i in seq_list:
# print i.dump()
#if
@@ -651,7 +652,7 @@ def describe(s1, s2, DNA=True):
# Nothing happened.
if not description:
- return [RawVar(DNA=DNA)]
+ return [RawVar(dna=dna)]
return description
#describe
diff --git a/mutalyzer/models.py b/mutalyzer/models.py
index b867b4306a346865d955014bb2a86f70f5df7493..50202aab26ae16c18f4deb1924161b988366ab5e 100644
--- a/mutalyzer/models.py
+++ b/mutalyzer/models.py
@@ -105,7 +105,7 @@ class RawVar(ComplexModel):
"""
__namespace__ = SOAP_NAMESPACE
- DNA = Mandatory.Boolean
+ dna = Mandatory.Boolean
start = Mandatory.Integer
start_offset = Mandatory.Integer
end = Mandatory.Integer
@@ -118,11 +118,11 @@ class RawVar(ComplexModel):
deleted = Mandatory.Unicode
inserted = Mandatory.Unicode
shift = Mandatory.Integer
- startAA = Mandatory.Unicode
- endAA = Mandatory.Unicode
+ start_aa = Mandatory.Unicode
+ end_aa = Mandatory.Unicode
term = Mandatory.Integer
hgvs = Mandatory.Unicode
- hgvsLength = Mandatory.Integer
+ hgvs_length = Mandatory.Integer
#RawVar