From ede6619d3b486727ab2000f86723f19d33aa1642 Mon Sep 17 00:00:00 2001
From: "J.F.J. Laros" <j.f.j.laros@lumc.nl>
Date: Fri, 28 Feb 2014 14:06:02 +0100
Subject: [PATCH] Added a generic insertion object, implemented rudimentary
transpositions.
---
mutalyzer/describe.py | 61 ++++++++++++++++++++++++++++++++++++++++---
1 file changed, 57 insertions(+), 4 deletions(-)
diff --git a/mutalyzer/describe.py b/mutalyzer/describe.py
index 0776989d..c9c30b60 100644
--- a/mutalyzer/describe.py
+++ b/mutalyzer/describe.py
@@ -160,6 +160,39 @@ def findFS(peptide, altPeptide, FS):
return maxFS - 1, fsStart
#findFS
+class Seq(object):
+ """
+ Container for an inserted sequence.
+ """
+ def __init__(self, sequence="", reference="", start=0, end=0,
+ reverse=False):
+ """
+ """
+ self.sequence = sequence
+ self.reference = reference
+ self.start = start
+ self.end = end
+ self.reverse = reverse
+ #__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 dump(self):
+ """
+ Debug function.
+ """
+ if self.sequence:
+ return self.sequence
+ return self.reference[self.start:self.end]
+ #dump
+#Seq
+
class RawVar(models.RawVar):
"""
Container for a raw variant.
@@ -485,7 +518,7 @@ def var2RawVar(s1, s2, var, DNA=True):
inserted=s2[var.sample_start:var.sample_end], type="delins")
# Inversion.
- if var.type == extractor.REVERSE_COMPLEMENT:
+ if var.type & extractor.REVERSE_COMPLEMENT:
trim = palinsnoop(s1[var.reference_start:var.reference_end])
if trim > 0: # Partial palindrome.
@@ -549,10 +582,30 @@ def describe(s1, s2, DNA=True):
#if
#if
else:
+ in_transposition = False
+
for variant in extractor.extract(unicode(s1), len(s1), unicode(s2), len(s2),
- 0):
- if variant.type != extractor.IDENTITY:
- description.append(var2RawVar(s1, s2, variant, DNA=DNA))
+ 0):
+ if variant.type & extractor.TRANSPOSITION_OPEN:
+ in_transposition = True
+ seq_list = []
+
+ if in_transposition:
+ if variant.type & extractor.IDENTITY:
+ seq_list.append(Seq(reference=s2, # This should be s1.
+ start=variant.sample_start, end=variant.sample_end,
+ reverse=variant.type & extractor.REVERSE_COMPLEMENT))
+ else:
+ seq_list.append(Seq(
+ sequence=s2[variant.sample_start:variant.sample_end]))
+ #if
+ elif variant.type != extractor.IDENTITY:
+ description.append(var2RawVar(s1, s2, variant, DNA=DNA))
+
+ if variant.type & extractor.TRANSPOSITION_CLOSE:
+ in_transposition = False
+ #for
+ #else
# Nothing happened.
if not description:
--
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