From 8ff7b0b60847e966ab3407106cad98a9f905feea Mon Sep 17 00:00:00 2001
From: "J.F.J. Laros" <j.f.j.laros@lumc.nl>
Date: Fri, 1 Aug 2014 18:13:40 +0200
Subject: [PATCH] Separated the variant classes from the description module.
---
mutalyzer/describe.py | 219 +-----------------------------------------
mutalyzer/variant.py | 218 +++++++++++++++++++++++++++++++++++++++++
2 files changed, 220 insertions(+), 217 deletions(-)
create mode 100644 mutalyzer/variant.py
diff --git a/mutalyzer/describe.py b/mutalyzer/describe.py
index b0b46842..bccd2f0d 100644
--- a/mutalyzer/describe.py
+++ b/mutalyzer/describe.py
@@ -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):
"""
diff --git a/mutalyzer/variant.py b/mutalyzer/variant.py
new file mode 100644
index 00000000..836c767b
--- /dev/null
+++ b/mutalyzer/variant.py
@@ -0,0 +1,218 @@
+"""
+"""
+
+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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