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Commit 61ddd6b7 authored by Laros's avatar Laros Committed by Vermaat
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Some more refactoring.

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mutalyzer/describe.py
+ 87
− 78
View file @ 61ddd6b7
......@@ -212,15 +212,14 @@ class Seq(object):
class SeqList(list):
def __str__(self):
representation = ';'.join(map(str, self))
if len(self) > 1:
return "[{}]".format(representation)
return representation
return "[{}]".format(';'.join(map(str, self)))
return str(self[0])
#__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)
......@@ -321,6 +320,7 @@ class DNAVar(models.DNAVar, HGVSVar):
variant stored in this class.
:rtype: int
"""
# NOTE: Obsolete?
if self.type in ("none", "unknown"): # `=' or `?'
return 1
......@@ -434,6 +434,7 @@ class ProteinVar(models.ProteinVar, HGVSVar):
variant stored in this class.
:rtype: int
"""
# NOTE: Obsolete?
if not self.start: # =
return 1
......@@ -477,6 +478,7 @@ class Allele(list):
:rtype: int
"""
# NOTE: Do we need to count the ; and [] ?
# NOTE: Obsolete?
return sum(map(lambda x: x.hgvs_length, self))
#length
#Allele
......@@ -571,7 +573,7 @@ def var_to_rawvar(s1, s2, var, seq_list=[], container=DNAVar):
sample_end=var.sample_end)
#var_to_rawvar
def describe(s1, s2, dna=True):
def describe_dna(s1, s2):
"""
Give an allele description of the change from {s1} to {s2}.
......@@ -584,84 +586,91 @@ def describe(s1, s2, dna=True):
:rtype: list(RawVar)
"""
description = Allele()
in_transposition = 0
for variant in extractor.extract(str(s1), len(s1), str(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)
if variant.type & extractor.TRANSPOSITION_OPEN:
if not in_transposition:
seq_list = SeqList()
in_transposition += 1
#if
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 in_transposition:
if variant.type & extractor.IDENTITY:
seq_list.append(Seq(start=variant.transposition_start + 1,
end=variant.transposition_end, reverse=False))
elif variant.type & extractor.REVERSE_COMPLEMENT:
seq_list.append(Seq(start=variant.transposition_start + 1,
end=variant.transposition_end, reverse=True))
else:
seq_list.append(Seq(
sequence=s2[variant.sample_start:variant.sample_end]))
#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(unicode(s1_part), len(s1_part),
unicode(s2_part), len(s2_part), 1):
description.append(var_to_rawvar(s1, s2, variant, container=ProteinVar))
if description:
description[-1].term = term + 2
description[-1].update()
elif not (variant.type & extractor.IDENTITY):
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))
#if
#for
return description
#describe_dna
def describe_protein(s1, s2):
"""
Give an allele description of the change from {s1} to {s2}.
:arg s1: Sequence 1.
:type s1: str
:arg s2: Sequence 2.
:type s2: str
:returns: A list of RawVar objects, representing the allele.
:rtype: list(RawVar)
"""
description = Allele()
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: # DNA description extraction, the only thing that `works'.
in_transposition = 0
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
if variant.type & extractor.TRANSPOSITION_OPEN:
if not in_transposition:
seq_list = SeqList()
in_transposition += 1
#if
if in_transposition:
if variant.type & extractor.IDENTITY:
seq_list.append(Seq(#reference=s1,
start=variant.transposition_start + 1,
end=variant.transposition_end, reverse=False))
elif variant.type & extractor.REVERSE_COMPLEMENT:
seq_list.append(Seq(#reference=s1,
start=variant.transposition_start + 1,
end=variant.transposition_end, reverse=True))
else:
seq_list.append(Seq(
sequence=s2[variant.sample_start:variant.sample_end]))
#if
elif not (variant.type & extractor.IDENTITY):
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))
#for i in seq_list:
# print i.dump()
#if
#for
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
# Nothing happened.
if not description:
return Allele(RawVar())
s1_part = s1
s2_part = s2
for variant in extractor.extract(str(s1_part), len(s1_part),
str(s2_part), len(s2_part), 1):
description.append(var_to_rawvar(s1, s2, variant,
container=ProteinVar))
if description:
description[-1].term = term + 2
description[-1].update()
#if
return description
#describe
#describe_protein
mutalyzer/entrypoints/mutalyzer.py
+ 11
− 11
View file @ 61ddd6b7
......@@ -100,28 +100,28 @@ def check_name(description):
reference_sequence = O.getIndexedOutput("original", 0)
sample_sequence = O.getIndexedOutput("mutated", 0)
extracted_allele = describe.describe(reference_sequence,
described_allele = describe.describe_dna(reference_sequence,
sample_sequence)
#extracted_protein_allele = describe.describe(
#described_protein_allele = describe.describe(
# O.getIndexedOutput("oldprotein", 0),
# O.getIndexedOutput("newprotein", 0, default=""),
# DNA=False)
extracted_protein_allele = ""
described_protein_allele = ""
extracted = extracted_protein = '(skipped)'
described = described_protein = '(skipped)'
if extracted_allele:
extracted = extracted_allele
if extracted_protein_allele:
extracted_protein = extracted_protein_allele
if described_allele:
described = described_allele
if described_protein_allele:
described_protein = described_protein_allele
print "\nExperimental services:"
print extracted
print extracted_protein
print described
print described_protein
#print "+++ %s" % O.getOutput("myTranscriptDescription")
print json.dumps({"reference_sequence": reference_sequence,
"sample_sequence": sample_sequence, "allele_description":
extracted_allele}, cls=MyEncoder)
described_allele}, cls=MyEncoder)
def main():
......
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