diff --git a/extras/soap-tools/describe.py b/extras/soap-tools/describe.py
new file mode 100644
index 0000000000000000000000000000000000000000..09a004e58c70fa878707c1aca748d4557ae14ba7
--- /dev/null
+++ b/extras/soap-tools/describe.py
@@ -0,0 +1,183 @@
+#!/usr/bin/python
+
+"""
+@requires: sys
+@requires: argparse
+@requires: Bio.Seq
+@requires: suds.client.Client
+"""
+
+
+import sys
+import argparse
+import Bio.Seq
+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
+
+WSDL_LOCATION = 'http://localhost/mutalyzer/services/?wsdl'
+
+def LongestCommonSubstring(S1, S2) :
+ """
+ """
+
+ M = [[0] * (len(S2) + 1) for i in xrange(len(S1) + 1)]
+ longest, x_longest = 0, 0
+
+ for x in xrange(1, len(S1) + 1) :
+ for y in xrange(1, len(S2) + 1) :
+ if S1[x - 1] == S2[y - 1] :
+ M[x][y] = M[x - 1][y - 1] + 1
+
+ if M[x][y] > longest :
+ longest = M[x][y]
+ x_longest = x
+ #if
+ #if
+ else :
+ M[x][y] = 0
+ #for
+ #for
+
+ return S1[x_longest - longest:x_longest]
+#LongestCommonSubstring
+
+def DNA_description(s1, s2, s1_start, s1_end, s2_start, s2_end) :
+ """
+ """
+ # TODO: Roll the variants to the 3' end.
+
+ # Nothing happened.
+ if s1 == s2:
+ return '='
+
+ # Insertion / Duplication.
+ if s1_start == s1_end :
+ ins_length = s2_end - s2_start
+
+ if s2_start - ins_length >= 0 and \
+ s1[s1_start - ins_length:s1_start] == s2[s2_start:s2_end] :
+
+ if ins_length == 1 :
+ return '%idup' % (s1_start)
+ return '%i_%idup' % (s1_start - ins_length + 1, s1_end)
+ #if
+ return '%i_%iins%s' % (s1_start, s1_start + 1, s2[s2_start:s2_end])
+ #if
+
+ # Deletion.
+ if s2_start == s2_end :
+ if s1_start + 1 == s1_end :
+ return '%idel' % (s1_start + 1)
+ return '%i_%idel' % (s1_start + 1, s1_end)
+ #if
+
+ # Substitution.
+ if s1_start + 1 == s1_end and s2_start + 1 == s2_end :
+ return '%i%s>%s' % (s1_start + 1, s1[s1_start], s2[s2_start])
+
+ # Simple InDel.
+ if s1_start + 1 == s1_end :
+ return '%idelins%s' % (s1_start + 1, s2[s2_start:s2_end])
+
+ # At this stage, we either have an inversion, an indel or a Compound
+ # variant.
+ lcs_f = LongestCommonSubstring(s1[s1_start:s1_end], s2[s2_start:s2_end])
+ lcs_r = LongestCommonSubstring(s1[s1_start:s1_end],
+ Bio.Seq.reverse_complement(s2[s2_start:s2_end]))
+ lcs_f_len = len(lcs_f)
+ lcs_r_len = len(lcs_r)
+
+ # 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 :
+
+ # Simple Inversion.
+ if s1_end - s1_start == lcs_r_len :
+ return '%i_%iinv' % (s1_start + 1, s1_end)
+
+ # Determine the position of the inversion in both the reference and
+ # the mutated sequence.
+ # The extra reverse_complement() is needed because searching for
+ # lcs_f in s2 might give a different result.
+ r1_len, r2_len = map(len, s1[s1_start:s1_end].split(lcs_r))
+ m1_len, m2_len = map(len,
+ Bio.Seq.reverse_complement(s2[s2_start:s2_end]).split(lcs_r))
+
+ # The flanks of the inversion (but not both) can be empty, so we
+ # generate descriptions conditionally.
+ leftVariant = ''
+ rightVariant = ''
+ # TODO: remove the lcs from the leftVariant and the lcp from the
+ # rightVariant.
+ if r1_len and m2_len :
+ leftVariant = '%s;' % DNA_description(s1, s2,
+ s1_start, s1_start + r1_len, s2_start, s2_start + m2_len)
+ if r2_len and m1_len :
+ rightVariant = ';%s' % DNA_description(s1, s2,
+ s1_end - r2_len, s1_end, s2_end - m1_len, s2_end)
+
+ return '%s%i_%iinv%s' % (leftVariant,
+ s1_start + r1_len + 1, s1_end - r2_len, rightVariant)
+ #if
+
+ # Compound variant.
+ else :
+ # Determine the position of the longest common substring in both
+ # the reference and the mutated sequence.
+ r1_len, r2_len = map(len, s1[s1_start:s1_end].split(lcs_f))
+ m1_len, m2_len = map(len, s2[s2_start:s2_end].split(lcs_f))
+
+ return '%s;%s' % (
+ DNA_description(s1, s2,
+ s1_start, s1_start + r1_len, s2_start, s2_start + m1_len),
+ DNA_description(s1, s2,
+ s1_end - r2_len, s1_end, s2_end - m2_len, s2_end))
+ #else
+ #if
+
+ # Default InDel.
+ return '%i_%idelins%s' % (s1_start + 1, s1_end, s2[s2_start:s2_end])
+#DNA_description
+
+def describe(description) :
+ """
+ """
+ service = Client(WSDL_LOCATION, cache = None).service
+ result = service.runMutalyzer(description)
+
+ s1 = str(result.original)
+ s2 = str(result.mutated)
+ lcp = len(longest_common_prefix(s1, s2))
+ lcs = len(longest_common_suffix(s1[lcp:], s2[lcp:]))
+ s1_end = len(s1) - lcs
+ s2_end = len(s2) - lcs
+
+ print(result.genomicDescription)
+ print(DNA_description(s1, s2, lcp, s1_end, lcp, s2_end))
+#describe
+
+def main() :
+ """
+ Main entry point.
+ """
+
+ parser = argparse.ArgumentParser(
+ prog = 'describe',
+ formatter_class = argparse.RawDescriptionHelpFormatter,
+ description = "",
+ epilog = "")
+
+ parser.add_argument('-d', dest = 'description', type = str,
+ required = True, help = 'HGVS description of a variant.')
+
+ arguments = parser.parse_args()
+
+ describe(arguments.description)
+#main
+
+if __name__ == "__main__" :
+ main()