From 6017ddd89d3e157ba8049c8f4bb3cb63f9f99659 Mon Sep 17 00:00:00 2001
From: "J.F.J. Laros" <j.f.j.laros@lumc.nl>
Date: Fri, 28 Feb 2014 17:39:03 +0100
Subject: [PATCH] Added a SeqList object. Finished first version of description
extractor.
---
mutalyzer/describe.py | 63 ++++++++++++++++++++++++++++++++++---------
1 file changed, 50 insertions(+), 13 deletions(-)
diff --git a/mutalyzer/describe.py b/mutalyzer/describe.py
index a3e7debe..d6069e77 100644
--- a/mutalyzer/describe.py
+++ b/mutalyzer/describe.py
@@ -193,6 +193,31 @@ class Seq(object):
#dump
#Seq
+class SeqList(object):
+ """
+ Container for a list of Seq objects.
+ """
+ def __init__(self, seq_list=[]):
+ self.seq_list = seq_list
+
+ def __str__(self):
+ representation = ';'.join(map(str, self.seq_list))
+
+ if len(self.seq_list) > 1:
+ return "[{}]".format(representation)
+ return representation
+ #__str__
+
+ def __len__(self):
+ return len(str(self))
+
+ def __iter__(self):
+ return iter(self.seq_list)
+
+ def append(self, item):
+ self.seq_list.append(item)
+#SeqList
+
class RawVar(models.RawVar):
"""
Container for a raw variant.
@@ -210,7 +235,7 @@ class RawVar(models.RawVar):
"""
def __init__(self, DNA=True, start=0, start_offset=0, end=0, end_offset=0,
- type="none", deleted="", inserted="", shift=0, startAA="", endAA="",
+ type="none", deleted="", inserted=None, shift=0, startAA="", endAA="",
term=0):
"""
Initialise the class with the appropriate values.
@@ -228,7 +253,7 @@ class RawVar(models.RawVar):
@arg deleted: Deleted part of the reference sequence.
@type deleted: unicode
@arg inserted: Inserted part.
- @type inserted: unicode
+ @type inserted: object
@arg shift: Amount of freedom.
@type shift: int
"""
@@ -454,7 +479,7 @@ def printpos(s, start, end, fill=0):
s[end:end + fs])
#printpos
-def var2RawVar(s1, s2, var, DNA=True):
+def var2RawVar(s1, s2, var, seq_list=[], DNA=True):
"""
"""
# Unknown.
@@ -484,8 +509,8 @@ def var2RawVar(s1, s2, var, DNA=True):
#if
return RawVar(DNA=DNA, start=var.reference_start,
end=var.reference_start + 1,
- inserted=s2[var.sample_start:var.sample_end], type="ins",
- shift=shift)
+ inserted=seq_list or SeqList(s2[var.sample_start:var.sample_end]),
+ type="ins", shift=shift)
#if
# Deletion.
@@ -515,7 +540,8 @@ def var2RawVar(s1, s2, var, DNA=True):
# Simple InDel.
if var.reference_start + 1 == var.reference_end:
return RawVar(DNA=DNA, start=var.reference_start + 1,
- inserted=s2[var.sample_start:var.sample_end], type="delins")
+ inserted=seq_list or s2[var.sample_start:var.sample_end],
+ type="delins")
# Inversion.
if var.type & extractor.REVERSE_COMPLEMENT:
@@ -532,8 +558,8 @@ def var2RawVar(s1, s2, var, DNA=True):
# InDel.
return RawVar(DNA=DNA, start=var.reference_start + 1,
- end=var.reference_end, inserted=s2[var.sample_start:var.sample_end],
- type="delins")
+ end=var.reference_end, inserted=seq_list or
+ s2[var.sample_start:var.sample_end], type="delins")
#var2RawVar
def describe(s1, s2, DNA=True):
@@ -586,24 +612,35 @@ def describe(s1, s2, DNA=True):
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
+
if variant.type & extractor.TRANSPOSITION_OPEN:
in_transposition = True
- seq_list = []
+ seq_list = SeqList()
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))
+ seq_list.append(Seq(reference=s1,
+ start=variant.sample_start + 1, end=variant.sample_end,
+ reverse=False))
+ elif variant.type & extractor.REVERSE_COMPLEMENT:
+ seq_list.append(Seq(reference=s1,
+ start=variant.sample_start + 1, end=variant.sample_end,
+ reverse=True))
else:
seq_list.append(Seq(
sequence=s2[variant.sample_start:variant.sample_end]))
#if
- elif variant.type != extractor.IDENTITY:
+ elif not (variant.type & extractor.IDENTITY):
description.append(var2RawVar(s1, s2, variant, DNA=DNA))
if variant.type & extractor.TRANSPOSITION_CLOSE:
in_transposition = False
+ description.append(var2RawVar(s1, s2, variant, seq_list,
+ DNA=DNA))
+ for i in seq_list:
+ print i.dump()
+ #if
#for
#else
--
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