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Commit 8ff7b0b6 authored by Laros's avatar Laros Committed by Vermaat
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Separated the variant classes from the description module.

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mutalyzer/describe.py
+ 2
− 217
View file @ 8ff7b0b6
......@@ -13,9 +13,8 @@ import collections
from Bio.SeqUtils import seq3
from Bio.Data import CodonTable
from mutalyzer.util import longest_common_prefix, longest_common_suffix
from mutalyzer.util import palinsnoop, roll, reverse_complement
from mutalyzer import models
from mutalyzer.util import palinsnoop, roll
from mutalyzer.variant import Seq, SeqList, DNAVar, ProteinVar, Allele
from extractor import extractor
......@@ -181,220 +180,6 @@ def find_fs(peptide, alternative_peptide, fs):
return max_fs - 1, fs_start
#find_fs
class Seq(object):
"""
Container for an inserted sequence.
"""
def __init__(self, sequence="", start=0, end=0, reverse=False):
"""
"""
self.sequence = sequence
self.start = start
self.end = end
self.reverse = reverse
self.type = "trans"
if self.sequence:
self.type = "ins"
#__init__
def __str__(self):
if self.sequence:
return self.sequence
inverted = "inv" if self.reverse else ""
return "{}_{}{}".format(self.start, self.end, inverted)
#__str__
def __nonzero__(self):
return bool(self.sequence)
#Seq
class SeqList(list):
def __str__(self):
if len(self) > 1:
return "[{}]".format(';'.join(map(str, self)))
return str(self[0])
#__str__
#SeqList
class DNAVar(models.DNAVar):
"""
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=SeqList([Seq()]),
inserted=SeqList([Seq()]), shift=0):
"""
Initialise the class with the appropriate values.
:arg start: Start position.
:type start: int
:arg start_offset:
:type start_offset: int
:arg end: End position.
:type end: int
:arg end_offset:
:type end_offset: int
:arg sample_start: Start position.
:type sample_start: int
:arg sample_start_offset:
:type sample_start_offset: int
:arg sample_end: End position.
:type sample_end: int
:arg sample_end_offset:
:type sample_end_offset: int
:arg type: Variant type.
:type type: unicode
:arg deleted: Deleted part of the reference sequence.
:type deleted: unicode
:arg inserted: Inserted part.
:type inserted: object
:arg shift: Amount of freedom.
:type shift: int
"""
# TODO: Will this container be used for all variants, or only genomic?
# start_offset and end_offset may be never used.
self.start = start
self.start_offset = start_offset
self.end = end
self.end_offset = end_offset
self.sample_start = sample_start
self.sample_start_offset = sample_start_offset
self.sample_end = sample_end
self.sample_end_offset = sample_end_offset
self.type = type
self.deleted = deleted
self.inserted = inserted
self.shift = shift
#__init__
def __str__(self):
"""
Give the HGVS description of the raw variant stored in this class.
:returns: The HGVS description of the raw variant stored in this class.
:rtype: unicode
"""
if self.type == "unknown":
return "?"
if self.type == "none":
return "="
description = "{}".format(self.start)
if self.start != self.end:
description += "_{}".format(self.end)
if self.type != "subst":
description += "{}".format(self.type)
if self.type in ("ins", "delins"):
return description + "{}".format(self.inserted)
return description
#if
return description + "{}>{}".format(self.deleted, self.inserted)
#__str__
#DNAVar
class ProteinVar(models.ProteinVar):
"""
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
#__init__
def __str__(self):
"""
Give 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 HGVS description of the raw variant stored in this class.
:rtype: unicode
"""
if self.type == "unknown":
return "?"
if self.type == "none":
return "="
description = ""
if not self.deleted:
if self.type == "ext":
description += '*'
else:
description += "{}".format(seq3(self.start_aa))
#if
else:
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 += self.type
if self.inserted:
description += "{}".format(seq3(self.inserted))
if self.type == "stop":
return description + '*'
if self.term:
return description + "fs*{}".format(self.term)
return description
#__str__
#ProteinVar
class Allele(list):
def __str__(self):
"""
Convert a list of raw variants to an HGVS allele description.
:returns: The HGVS description of {allele}.
:rtype: str
"""
if len(self) > 1:
return "[{}]".format(';'.join(map(lambda x: str(x), self)))
return str(self[0])
#__str__
#Allele
def var_to_rawvar(s1, s2, var, seq_list=[], container=DNAVar):
"""
......
mutalyzer/variant.py 0 → 100644
+ 218
− 0
View file @ 8ff7b0b6
"""
"""
from mutalyzer import models
class Seq(object):
"""
Container for an inserted sequence.
"""
def __init__(self, sequence="", start=0, end=0, reverse=False):
"""
"""
self.sequence = sequence
self.start = start
self.end = end
self.reverse = reverse
self.type = "trans"
if self.sequence:
self.type = "ins"
#__init__
def __str__(self):
if self.sequence:
return self.sequence
inverted = "inv" if self.reverse else ""
return "{}_{}{}".format(self.start, self.end, inverted)
#__str__
def __nonzero__(self):
return bool(self.sequence)
#Seq
class SeqList(list):
def __str__(self):
if len(self) > 1:
return "[{}]".format(';'.join(map(str, self)))
return str(self[0])
#__str__
#SeqList
class DNAVar(models.DNAVar):
"""
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=SeqList([Seq()]),
inserted=SeqList([Seq()]), shift=0):
"""
Initialise the class with the appropriate values.
:arg start: Start position.
:type start: int
:arg start_offset:
:type start_offset: int
:arg end: End position.
:type end: int
:arg end_offset:
:type end_offset: int
:arg sample_start: Start position.
:type sample_start: int
:arg sample_start_offset:
:type sample_start_offset: int
:arg sample_end: End position.
:type sample_end: int
:arg sample_end_offset:
:type sample_end_offset: 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
"""
# TODO: Will this container be used for all variants, or only genomic?
# start_offset and end_offset may be never used.
self.start = start
self.start_offset = start_offset
self.end = end
self.end_offset = end_offset
self.sample_start = sample_start
self.sample_start_offset = sample_start_offset
self.sample_end = sample_end
self.sample_end_offset = sample_end_offset
self.type = type
self.deleted = deleted
self.inserted = inserted
self.shift = shift
#__init__
def __str__(self):
"""
Give the HGVS description of the raw variant stored in this class.
:returns: The HGVS description of the raw variant stored in this class.
:rtype: str
"""
if self.type == "unknown":
return "?"
if self.type == "none":
return "="
description = "{}".format(self.start)
if self.start != self.end:
description += "_{}".format(self.end)
if self.type != "subst":
description += "{}".format(self.type)
if self.type in ("ins", "delins"):
return description + "{}".format(self.inserted)
return description
#if
return description + "{}>{}".format(self.deleted, self.inserted)
#__str__
#DNAVar
class ProteinVar(models.ProteinVar):
"""
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
#__init__
def __str__(self):
"""
Give 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 HGVS description of the raw variant stored in this class.
:rtype: str
"""
if self.type == "unknown":
return "?"
if self.type == "none":
return "="
description = ""
if not self.deleted:
if self.type == "ext":
description += '*'
else:
description += "{}".format(seq3(self.start_aa))
#if
else:
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 += self.type
if self.inserted:
description += "{}".format(seq3(self.inserted))
if self.type == "stop":
return description + '*'
if self.term:
return description + "fs*{}".format(self.term)
return description
#__str__
#ProteinVar
class Allele(list):
def __str__(self):
"""
Convert a list of raw variants to an HGVS allele description.
:returns: The HGVS description of {allele}.
:rtype: str
"""
if len(self) > 1:
return "[{}]".format(';'.join(map(lambda x: str(x), self)))
return str(self[0])
#__str__
#Allele
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