From bfc3f7cb0228a2c01c2bbb7e3c5cc8a0bc13f1a8 Mon Sep 17 00:00:00 2001
From: "J.F.J. Laros" <j.f.j.laros@lumc.nl>
Date: Sun, 22 Jan 2012 20:45:33 +0000
Subject: [PATCH] Added rolling for insertions and deletions. Needs checking.
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@442 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
extras/soap-tools/describe.py | 35 +++++++++++++++++++++++++++++------
1 file changed, 29 insertions(+), 6 deletions(-)
diff --git a/extras/soap-tools/describe.py b/extras/soap-tools/describe.py
index 893339bd..b6f2c8bd 100644
--- a/extras/soap-tools/describe.py
+++ b/extras/soap-tools/describe.py
@@ -15,6 +15,7 @@ from suds.client import Client
from mutalyzer.util import monkey_patch_suds; monkey_patch_suds()
from mutalyzer.util import longest_common_prefix, longest_common_suffix
+from mutalyzer.util import palinsnoop, roll
WSDL_LOCATION = "http://localhost/mutalyzer/services/?wsdl"
@@ -49,8 +50,6 @@ def LongestCommonSubstring(s1, s2) :
def DNA_description(s1, s2, s1_start, s1_end, s2_start, s2_end) :
"""
"""
- # TODO: Roll the variants to the 3' end.
- # TODO: Palindrome snooping.
# Nothing happened.
if s1 == s2:
@@ -59,6 +58,12 @@ def DNA_description(s1, s2, s1_start, s1_end, s2_start, s2_end) :
# Insertion / Duplication.
if s1_start == s1_end :
ins_length = s2_end - s2_start
+ dummy, shift = roll(s2, s2_start + 1, s2_end + 1)
+
+ s1_start += shift + 1
+ s1_end += shift + 1
+ s2_start += shift + 1
+ s2_end += shift + 1
if s2_start - ins_length >= 0 and \
s1[s1_start - ins_length:s1_start] == s2[s2_start:s2_end] :
@@ -72,9 +77,11 @@ def DNA_description(s1, s2, s1_start, s1_end, s2_start, s2_end) :
# Deletion.
if s2_start == s2_end :
+ dummy, shift = roll(s1, s1_start + 1, s1_end)
+
if s1_start + 1 == s1_end :
- return "%idel" % (s1_start + 1)
- return "%i_%idel" % (s1_start + 1, s1_end)
+ return "%idel" % (s1_start + shift + 1)
+ return "%i_%idel" % (s1_start + shift + 1, s1_end + shift)
#if
# Substitution.
@@ -87,20 +94,31 @@ def DNA_description(s1, s2, s1_start, s1_end, s2_start, s2_end) :
# At this stage, we either have an inversion, an indel or a Compound
# variant.
- # NOTE: We might want to do a palindrome snoop in the second line.
s1_end_f, s2_end_f, lcs_f_len = LongestCommonSubstring(s1[s1_start:s1_end],
s2[s2_start:s2_end])
s1_end_r, s2_end_r, lcs_r_len = LongestCommonSubstring(s1[s1_start:s1_end],
Bio.Seq.reverse_complement(s2[s2_start:s2_end]))
+ # Palindrome snooping.
+ trim = palinsnoop(s1[s1_start + s1_end_r - lcs_r_len:s1_start + s1_end_r])
+ if trim < 0 : # Full palindrome.
+ lcs_r_len = 0 # s1_end_r and s2_end_r should not be used after this.
+
# Inversion or Compound variant.
if max(lcs_f_len, lcs_r_len) > 3 : # TODO: This is not a good criterium.
# Inversion.
if lcs_f_len <= lcs_r_len :
+ if trim > 0 : # Partial palindrome.
+ s1_end_r -= trim
+ s2_end_r -= trim
+ lcs_r_len -= 2 * trim
+ #if
+
# Simple Inversion.
- if s1_end - s1_start == lcs_r_len :
+ if s2_end - s2_start == lcs_r_len and \
+ s1_end - s1_start == lcs_r_len :
return "%i_%iinv" % (s1_start + 1, s1_end)
r1_len = s1_end_r - lcs_r_len
@@ -165,6 +183,11 @@ def describe(description) :
s1_end = len(s1) - lcs
s2_end = len(s2) - lcs
+ for i in result.rawVariants.RawVariant :
+ print i.description
+ print i.visualisation
+ print
+ #for
print(result.genomicDescription)
print(DNA_description(s1, s2, lcp, s1_end, lcp, s2_end))
#describe
--
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