From 378d6365d702070aeaa05741a3435a8cf0295b6c Mon Sep 17 00:00:00 2001
From: "Jeroen F.J. Laros" <jlaros@fixedpoint.nl>
Date: Sun, 19 Apr 2015 13:07:37 +0200
Subject: [PATCH] Processed various comments, PEP8.
---
mutalyzer/describe.py | 75 +++++++++---------------
mutalyzer/variant.py | 130 ++++++++++++++++++++----------------------
2 files changed, 91 insertions(+), 114 deletions(-)
diff --git a/mutalyzer/describe.py b/mutalyzer/describe.py
index 09c133d8..2a12e8ea 100644
--- a/mutalyzer/describe.py
+++ b/mutalyzer/describe.py
@@ -1,8 +1,6 @@
"""
-Prototype of a module that can generate a HGVS description of the variant(s)
-leading from one sequence to an other.
-
-@requires: Bio.Seq
+Generate a HGVS description of the variant(s) leading from one sequence to an
+other.
"""
@@ -23,10 +21,10 @@ 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
+ # visualisation in the _visualise() function of mutator.py
fs = 10 # Flank size.
- return "{} {}{} {}".format(s[start - fs:start], s[start:end], '-' * fill,
+ return '{} {}{} {}'.format(s[start - fs:start], s[start:end], '-' * fill,
s[end:end + fs])
@@ -61,9 +59,9 @@ def make_fs_tables(table_id):
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
-#make_fs_tables
+
def _peptide_overlaps(peptide):
"""
@@ -75,8 +73,8 @@ def _peptide_overlaps(peptide):
:returns: All 2-mers of {peptide} in order of appearance.
:rtype: list(unicode)
"""
- return map(lambda x: peptide[x:x+2], range(len(peptide) - 1))
-#_peptide_overlaps
+ return [a + b for (a, b) in zip(peptide, peptide[1:])]
+
def _options(peptide_overlaps, peptide_prefix, fs, output):
"""
@@ -94,10 +92,10 @@ def _options(peptide_overlaps, peptide_prefix, fs, output):
if not peptide_overlaps:
output.append(peptide_prefix)
return
- #if
+
for i in fs[peptide_overlaps[0]]:
_options(peptide_overlaps[1:], peptide_prefix + i, fs, output)
-#_options
+
def enum_fs(peptide, fs):
"""
@@ -113,9 +111,9 @@ def enum_fs(peptide, fs):
"""
output = []
- _options(_peptide_overlaps(peptide), "", fs, output)
+ _options(_peptide_overlaps(peptide), '', fs, output)
return output
-#enum_fs
+
def fit_fs(peptide, alternative_peptide, fs):
"""
@@ -145,7 +143,7 @@ def fit_fs(peptide, alternative_peptide, fs):
if not alternative_peptide[i] in fs[peptide_overlaps[i]]:
return False
return True
-#fit_fs
+
def find_fs(peptide, alternative_peptide, fs):
"""
@@ -173,11 +171,8 @@ def find_fs(peptide, alternative_peptide, fs):
if j >= max_fs:
max_fs = j
fs_start = i - j + 2
- #if
- #for
return max_fs - 1, fs_start
-#find_fs
def var_to_rawvar(s1, s2, var, seq_list=[], container=DNAVar,
@@ -186,7 +181,7 @@ def var_to_rawvar(s1, s2, var, seq_list=[], container=DNAVar,
"""
# Unknown.
if s1 == '?' or s2 == '?':
- return [container(type="unknown", weight_position=weight_position)]
+ return [container(type='unknown', weight_position=weight_position)]
# Insertion / Duplication.
if var.reference_start == var.reference_end:
@@ -200,27 +195,25 @@ def var_to_rawvar(s1, s2, var, seq_list=[], container=DNAVar,
var.sample_end += shift3
if (var.sample_start - ins_length >= 0 and
- s1[var.reference_start - ins_length:var.reference_start] ==
- s2[var.sample_start:var.sample_end]):
-
+ s1[var.reference_start - ins_length:var.reference_start] ==
+ s2[var.sample_start:var.sample_end]):
# NOTE: We may want to omit the inserted / deleted sequence and
# use the ranges instead.
return container(start=var.reference_start - ins_length + 1,
- end=var.reference_end, type="dup", shift=shift,
+ end=var.reference_end, type='dup', shift=shift,
sample_start=var.sample_start + 1, sample_end=var.sample_end,
inserted=ISeqList([ISeq(sequence=s2[
var.sample_start:var.sample_end],
weight_position=weight_position)]),
weight_position=weight_position)
- #if
+
return container(start=var.reference_start,
end=var.reference_start + 1,
inserted=seq_list or
ISeqList([ISeq(sequence=s2[var.sample_start:var.sample_end],
weight_position=weight_position)]),
- type="ins", shift=shift, sample_start=var.sample_start + 1,
+ type='ins', shift=shift, sample_start=var.sample_start + 1,
sample_end=var.sample_end, weight_position=weight_position)
- #if
# Deletion.
if var.sample_start == var.sample_end:
@@ -231,27 +224,24 @@ def var_to_rawvar(s1, s2, var, seq_list=[], container=DNAVar,
var.reference_end += shift3
return container(start=var.reference_start + 1,
- end=var.reference_end, type="del", shift=shift,
+ end=var.reference_end, type='del', shift=shift,
sample_start=var.sample_start, sample_end=var.sample_end + 1,
deleted=ISeqList([ISeq(sequence=s1[
var.reference_start:var.reference_end],
weight_position=weight_position)]),
weight_position=weight_position)
- #if
# Substitution.
if (var.reference_start + 1 == var.reference_end and
- var.sample_start + 1 == var.sample_end):
-
+ var.sample_start + 1 == var.sample_end):
return container(start=var.reference_start + 1,
end=var.reference_end, sample_start=var.sample_start + 1,
- sample_end=var.sample_end, type="subst",
+ sample_end=var.sample_end, type='subst',
deleted=ISeqList([ISeq(sequence=s1[var.reference_start],
weight_position=weight_position)]),
inserted=ISeqList([ISeq(sequence=s2[var.sample_start],
weight_position=weight_position)]),
weight_position=weight_position)
- #if
# Inversion.
if var.type & extractor.REVERSE_COMPLEMENT:
@@ -260,10 +250,9 @@ def var_to_rawvar(s1, s2, var, seq_list=[], container=DNAVar,
if trim > 0: # Partial palindrome.
var.reference_end -= trim
var.sample_end -= trim
- #if
return container(start=var.reference_start + 1,
- end=var.reference_end, type="inv",
+ end=var.reference_end, type='inv',
sample_start=var.sample_start + 1, sample_end=var.sample_end,
deleted=ISeqList([ISeq(sequence=s1[
var.reference_start:var.reference_end],
@@ -272,7 +261,6 @@ def var_to_rawvar(s1, s2, var, seq_list=[], container=DNAVar,
var.sample_start:var.reference_end],
weight_position=weight_position)]),
weight_position=weight_position)
- #if
# InDel.
return container(start=var.reference_start + 1,
@@ -282,9 +270,9 @@ def var_to_rawvar(s1, s2, var, seq_list=[], container=DNAVar,
inserted=seq_list or
ISeqList([ISeq(sequence=s2[var.sample_start:var.sample_end],
weight_position=weight_position)]),
- type="delins", sample_start=var.sample_start + 1,
+ type='delins', sample_start=var.sample_start + 1,
sample_end=var.sample_end, weight_position=weight_position)
-#var_to_rawvar
+
def describe_dna(s1, s2):
"""
@@ -302,7 +290,7 @@ def describe_dna(s1, s2):
in_transposition = 0
extracted = extractor.extract(s1.encode('utf-8'), len(s1),
- s2.encode('utf-8'), len(s2), 0)
+ s2.encode('utf-8'), len(s2), 0)
for variant in extracted.variants:
# print (variant.type, variant.reference_start,
# variant.reference_end, variant.sample_start,
@@ -315,7 +303,6 @@ def describe_dna(s1, s2):
if not in_transposition:
seq_list = ISeqList()
in_transposition += 1
- #if
if in_transposition:
if variant.type & extractor.IDENTITY:
@@ -330,7 +317,6 @@ def describe_dna(s1, s2):
seq_list.append(ISeq(
sequence=s2[variant.sample_start:variant.sample_end],
weight_position=extracted.weight_position))
- #if
elif not (variant.type & extractor.IDENTITY):
description.append(var_to_rawvar(s1, s2, variant,
weight_position=extracted.weight_position))
@@ -341,13 +327,11 @@ def describe_dna(s1, s2):
if not in_transposition:
description.append(var_to_rawvar(s1, s2, variant, seq_list,
weight_position=extracted.weight_position))
- #if
- #for
if not description:
return Allele([DNAVar()])
return description
-#describe_dna
+
def describe_protein(s1, s2):
"""
@@ -373,19 +357,17 @@ def describe_protein(s1, s2):
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) - 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(s1_part.encode('utf-8'), len(s1_part),
- s2_part.encode('utf-8'), len(s2_part), 1):
+ s2_part.encode('utf-8'), len(s2_part), 1):
description.append(var_to_rawvar(s1, s2, variant,
container=ProteinVar))
@@ -393,4 +375,3 @@ def describe_protein(s1, s2):
description[-1].term = term + 2
return description
-#describe_protein
diff --git a/mutalyzer/variant.py b/mutalyzer/variant.py
index ab7a5e85..5b84b3dc 100644
--- a/mutalyzer/variant.py
+++ b/mutalyzer/variant.py
@@ -7,26 +7,26 @@ from Bio.SeqUtils import seq3
from extractor import extractor
-from mutalyzer import models
-
-weights = {
- "subst": extractor.WEIGHT_SUBSTITUTION,
- "del": extractor.WEIGHT_DELETION,
- "ins": extractor.WEIGHT_INSERTION,
- "dup": extractor.WEIGHT_INSERTION,
- "inv": extractor.WEIGHT_INVERSION,
- "delins": extractor.WEIGHT_DELETION_INSERTION
+
+WEIGHTS = {
+ 'subst': extractor.WEIGHT_SUBSTITUTION,
+ 'del': extractor.WEIGHT_DELETION,
+ 'ins': extractor.WEIGHT_INSERTION,
+ 'dup': extractor.WEIGHT_INSERTION,
+ 'inv': extractor.WEIGHT_INVERSION,
+ 'delins': extractor.WEIGHT_DELETION_INSERTION
}
+
class HGVSList(list):
"""
Container for a list of sequences or variants.
"""
def __unicode__(self):
if len(self) > 1:
- return "[{}]".format(';'.join(map(unicode, self)))
+ return '[{}]'.format(';'.join(map(unicode, self)))
return unicode(self[0])
- #__unicode__
+
def weight(self):
weight = sum(map(lambda x: x.weight(), self))
@@ -34,20 +34,21 @@ class HGVSList(list):
if len(self) > 1:
return weight + (len(self) + 1) * extractor.WEIGHT_SEPARATOR
return weight
- #weight
-#HGVSList
+
class Allele(HGVSList):
pass
+
class ISeqList(HGVSList):
pass
+
class ISeq(object):
"""
Container for an inserted sequence.
"""
- def __init__(self, sequence="", start=0, end=0, reverse=False,
+ def __init__(self, sequence='', start=0, end=0, reverse=False,
weight_position=1):
"""
:arg sequence: Literal inserted sequence.
@@ -65,42 +66,42 @@ class ISeq(object):
self.reverse = reverse
self.weight_position = weight_position
- self.type = "trans"
+ self.type = 'trans'
if self.sequence:
- self.type = "ins"
- #__init__
+ self.type = 'ins'
+
def __unicode__(self):
- if self.type == "ins":
+ if self.type == 'ins':
return self.sequence
if not (self.start or self.end):
- return ""
+ return ''
+
+ inverted = 'inv' if self.reverse else ''
+ return '{}_{}{}'.format(self.start, self.end, inverted)
- inverted = "inv" if self.reverse else ""
- return "{}_{}{}".format(self.start, self.end, inverted)
- #__unicode__
def __nonzero__(self):
return bool(self.sequence)
+
def weight(self):
- if self.type == "ins":
+ if self.type == 'ins':
return len(self.sequence) * extractor.WEIGHT_BASE
- inverse_weight = weights["inv"] if self.reverse else 0
+ inverse_weight = WEIGHTS['inv'] if self.reverse else 0
return (self.weight_position * 2 + extractor.WEIGHT_SEPARATOR +
inverse_weight)
- #weight
-#ISeq
-class DNAVar(models.DNAVar):
+
+class DNAVar(object):
"""
Container for a DNA variant.
"""
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=ISeqList([ISeq()]),
+ sample_end_offset=0, type='none', deleted=ISeqList([ISeq()]),
inserted=ISeqList([ISeq()]), shift=0, weight_position=1):
"""
Initialise the class with the appropriate values.
@@ -145,7 +146,7 @@ class DNAVar(models.DNAVar):
self.inserted = inserted
self.weight_position = weight_position
self.shift = shift
- #__init__
+
def __unicode__(self):
"""
@@ -154,47 +155,45 @@ class DNAVar(models.DNAVar):
:returns: The HGVS description of the raw variant stored in this class.
:rtype: unicode
"""
- if self.type == "unknown":
- return "?"
- if self.type == "none":
- return "="
+ if self.type == 'unknown':
+ return '?'
+ if self.type == 'none':
+ return '='
- description = "{}".format(self.start)
+ description = '{}'.format(self.start)
if self.start != self.end:
- description += "_{}".format(self.end)
+ description += '_{}'.format(self.end)
- if self.type != "subst":
- description += "{}".format(self.type)
+ if self.type != 'subst':
+ description += '{}'.format(self.type)
- if self.type in ("ins", "delins"):
- return description + "{}".format(self.inserted)
+ if self.type in ('ins', 'delins'):
+ return description + '{}'.format(self.inserted)
return description
- #if
- return description + "{}>{}".format(self.deleted, self.inserted)
- #__unicode__
+ return description + '{}>{}'.format(self.deleted, self.inserted)
+
def weight(self):
- if self.type == "unknown":
+ if self.type == 'unknown':
return -1
- if self.type == "none":
+ if self.type == 'none':
return 0
weight = self.weight_position
if self.start != self.end:
weight += self.weight_position + extractor.WEIGHT_SEPARATOR
- return weight + weights[self.type] + self.inserted.weight()
- #weight
-#DNAVar
+ return weight + WEIGHTS[self.type] + self.inserted.weight()
+
-class ProteinVar(models.ProteinVar):
+class ProteinVar(object):
"""
Container for a protein variant.
"""
def __init__(self, start=0, end=0, sample_start=0, sample_end=0,
- type="none", deleted=ISeqList([ISeq()]),
+ type='none', deleted=ISeqList([ISeq()]),
inserted=ISeqList([ISeq()]), shift=0, term=0):
"""
Initialise the class with the appropriate values.
@@ -227,7 +226,7 @@ class ProteinVar(models.ProteinVar):
self.inserted = inserted
self.shift = shift
self.term = term
- #__init__
+
def __unicode__(self):
"""
@@ -239,32 +238,29 @@ class ProteinVar(models.ProteinVar):
:returns: The HGVS description of the raw variant stored in this class.
:rtype: unicode
"""
- if self.type == "unknown":
- return "?"
- if self.type == "none":
- return "="
+ if self.type == 'unknown':
+ return '?'
+ if self.type == 'none':
+ return '='
- description = ""
+ description = ''
if not self.deleted:
- if self.type == "ext":
+ if self.type == 'ext':
description += '*'
else:
- description += "{}".format(seq3(self.start_aa))
- #if
+ description += '{}'.format(seq3(self.start_aa))
else:
- description += "{}".format(seq3(self.deleted))
- description += "{}".format(self.start)
+ description += '{}'.format(seq3(self.deleted))
+ 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
+ description += '_{}{}'.format(seq3(self.end_aa), self.end)
+ 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))
+ description += '{}'.format(seq3(self.inserted))
- if self.type == "stop":
+ if self.type == 'stop':
return description + '*'
if self.term:
- return description + "fs*{}".format(self.term)
+ return description + 'fs*{}'.format(self.term)
return description
- #__unicode__
-#ProteinVar
--
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