Minor (punctuation) changes in the about page.

Modified describe.py to comply with the preferred programming style.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@594 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

mutalyzer/describe.py

@@ -12,24 +12,23 @@ from mutalyzer.util import longest_common_prefix, longest_common_suffix
 from mutalyzer.util import palinsnoop, roll
 from mutalyzer import models
 
-def LCSMatrix(s1, s2) :
+def LCSMatrix(s1, s2):
     """
     Todo: Not yet in use.
     """
-
     y_max = len(s1) + 1
     x_max = len(s2) + 1
     M = [[0] * x_max for i in xrange(y_max)]
 
-    for x in xrange(1, y_max) :
-        for y in xrange(1, x_max) :
-            if s1[x - 1] == s2[y - 1] :
+    for x in xrange(1, y_max):
+        for y in xrange(1, x_max):
+            if s1[x - 1] == s2[y - 1]:
                 M[x][y] = M[x - 1][y - 1] + 1
 
     return M
 #LCSMatrix
 
-def findMax(M, x1, x2, y1, y2) :
+def findMax(M, x1, x2, y1, y2):
     """
     M = describe.LCSMatrix("banaan", "ana")
 
@@ -41,17 +40,16 @@ def findMax(M, x1, x2, y1, y2) :
 
     Todo: Not yet in use.
     """
-
     longest, x_longest, y_longest = 0, 0, 0
 
-    for x in xrange(x1, x2) :
+    for x in xrange(x1, x2):
         x_relative = x - x1
 
-        for y in xrange(y1, y2) :
+        for y in xrange(y1, y2):
             y_relative = y - y1
             realVal = min(x_relative, y_relative, M[x][y])
 
-            if realVal > longest :
+            if realVal > longest:
                 longest = realVal
                 x_longest = x_relative
                 y_longest = y_relative
@@ -62,7 +60,7 @@ def findMax(M, x1, x2, y1, y2) :
     return x_longest, y_longest, longest
 #findMax
 
-def LongestCommonSubstring(s1, s2) :
+def LongestCommonSubstring(s1, s2):
     """
     Find the longest common substring between {s1} and {s2}.
 
@@ -78,18 +76,17 @@ def LongestCommonSubstring(s1, s2) :
     @returns: The end locations and the length of the longest common substring.
     @rtype: tuple(int, int, int)
     """
-
     len_s1 = len(s1)
     len_s2 = len(s2)
     M = [[0] * (len_s2 + 1) for i in xrange(len_s1 + 1)]
     longest, x_longest, y_longest = 0, 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] :
+    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 :
+                if M[x][y] > longest:
                     longest = M[x][y]
                     x_longest = x
                     y_longest = y
@@ -103,7 +100,7 @@ def LongestCommonSubstring(s1, s2) :
     return x_longest, y_longest, longest
 #LongestCommonSubstring
 
-class RawVar(models.RawVar) :
+class RawVar(models.RawVar):
     """
     Container for a raw variant.
 
@@ -116,7 +113,7 @@ class RawVar(models.RawVar) :
     """
 
     def __init__(self, start=0, start_offset=0, end=0, end_offset=0,
-        type="none", deleted="", inserted="", shift=0, hgvs="") :
+        type="none", deleted="", inserted="", shift=0):
         """
         Initialise the class with the appropriate values.
 
@@ -139,7 +136,6 @@ class RawVar(models.RawVar) :
         """
         # 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
@@ -148,10 +144,10 @@ class RawVar(models.RawVar) :
         self.deleted = deleted
         self.inserted = inserted
         self.shift = shift
-        self.hgvs = hgvs
+        self.hgvs = self.description()
     #__init__
 
-    def description(self) :
+    def description(self):
         """
         Give the HGVS description of the raw variant stored in this class.
 
@@ -161,19 +157,18 @@ class RawVar(models.RawVar) :
         @returns: The HGVS description of the raw variant stored in this class.
         @rtype: str
         """
-
-        if not self.start :
+        if not self.start:
             return "="
 
         descr = "%i" % self.start
 
-        if self.end :
+        if self.end:
             descr += "_%i" % self.end
 
-        if self.type != "subst" :
+        if self.type != "subst":
             descr += "%s" % self.type
 
-            if self.inserted :
+            if self.inserted:
                 return descr + "%s" % self.inserted
             return descr
         #if
@@ -181,7 +176,7 @@ class RawVar(models.RawVar) :
         return descr + "%s>%s" % (self.deleted, self.inserted)
     #description
 
-    def descriptionLength(self) :
+    def descriptionLength(self):
         """
         Give the standardised length of the HGVS description of the raw variant
         stored in this class.
@@ -193,7 +188,6 @@ class RawVar(models.RawVar) :
             variant stored in this class.
         @rtype: int
         """
-
         if not self.start : # =
             return 1
 
@@ -202,22 +196,19 @@ class RawVar(models.RawVar) :
         if self.end : # '_' and end position.
             descrLen += 2
 
-        if self.type != "subst" :
+        if self.type != "subst":
             descrLen += len(self.type)
 
-            if self.inserted :
+            if self.inserted:
                 return descrLen + len(self.inserted)
             return descrLen
         #if
 
         return 4 # Start position, '>' and end position.
     #descriptionLength
-
-    def putHGVS(self):
-        self.hgvs = self.description()
 #RawVar
 
-def alleleDescription(allele) :
+def alleleDescription(allele):
     """
     Convert a list of raw variants to an HGVS allele description.
 
@@ -227,13 +218,12 @@ def alleleDescription(allele) :
     @returns: The HGVS description of {allele}.
     @rval: str
     """
-
-    if len(allele) > 1 :
+    if len(allele) > 1:
         return "[%s]" % ';'.join(map(lambda x : x.hgvs, allele))
     return allele[0].hgvs
 #alleleDescription
 
-def alleleDescriptionLength(allele) :
+def alleleDescriptionLength(allele):
     """
     Calculate the standardised length of an HGVS allele description.
 
@@ -243,24 +233,22 @@ def alleleDescriptionLength(allele) :
     @returns: The standardised length of the HGVS description of {allele}.
     @rval: int
     """
-
     return sum(map(lambda x : x.descriptionLength(), allele))
 #alleleDescriptionLength
 
-def printpos(s, start, end, fill = 0) :
+def printpos(s, start, end, fill = 0):
     """
     For debugging purposes.
     """
     # TODO: See if this can partially replace or be merged with the
     #       visualisation in the __mutate() function of mutator.py
-
     fs = 10 # Flank size.
 
     return "%s %s%s %s" % (s[start - fs:start], s[start:end], '-' * fill,
         s[end:end + fs])
 #printpos
 
-def DNA_description(M, s1, s2, s1_start, s1_end, s2_start, s2_end) :
+def DNA_description(M, s1, s2, s1_start, s1_end, s2_start, s2_end):
     """
     Give an allele description of the change from {s1} to {s2} in the range
     {s1_start}..{s1_end} on {s1} and {s2_start}..{s2_end} on {s2}.
@@ -290,7 +278,7 @@ def DNA_description(M, s1, s2, s1_start, s1_end, s2_start, s2_end) :
         return [RawVar()]
 
     # Insertion / Duplication.
-    if s1_start == s1_end :
+    if s1_start == s1_end:
         ins_length = s2_end - s2_start
         shift5, shift3 = roll(s2, s2_start + 1, s2_end)
         shift = shift5 + shift3
@@ -301,40 +289,39 @@ def DNA_description(M, s1, s2, s1_start, s1_end, s2_start, s2_end) :
         s2_end += shift3
 
         if s2_start - ins_length >= 0 and \
-            s1[s1_start - ins_length:s1_start] == s2[s2_start:s2_end] :
+            s1[s1_start - ins_length:s1_start] == s2[s2_start:s2_end]:
 
-            if ins_length == 1 :
-                return [RawVar(start = s1_start, type = "dup", shift = shift)]
-            return [RawVar(start = s1_start - ins_length + 1, end = s1_end,
-                type = "dup", shift = shift)]
+            if ins_length == 1:
+                return [RawVar(start=s1_start, type="dup", shift=shift)]
+            return [RawVar(start=s1_start - ins_length + 1, end=s1_end,
+                type="dup", shift=shift)]
         #if
-        return [RawVar(start = s1_start, end = s1_start + 1,
-            inserted = s2[s2_start:s2_end], type = "ins", shift = shift)]
+        return [RawVar(start=s1_start, end=s1_start + 1,
+            inserted=s2[s2_start:s2_end], type="ins", shift=shift)]
     #if
 
     # Deletion.
-    if s2_start == s2_end :
+    if s2_start == s2_end:
         shift5, shift3 = roll(s1, s1_start + 1, s1_end)
         shift = shift5 + shift3
 
         s1_start += shift3 + 1
         s1_end += shift3
 
-        if s1_start == s1_end :
-            return [RawVar(start = s1_start, type = "del", shift = shift)]
-        return [RawVar(start = s1_start, end = s1_end, type = "del",
-            shift = shift)]
+        if s1_start == s1_end:
+            return [RawVar(start=s1_start, type="del", shift=shift)]
+        return [RawVar(start=s1_start, end=s1_end, type="del", shift=shift)]
     #if
 
     # Substitution.
-    if s1_start + 1 == s1_end and s2_start + 1 == s2_end :
-        return [RawVar(start = s1_start + 1, deleted = s1[s1_start],
-            inserted = s2[s2_start], type = "subst")]
+    if s1_start + 1 == s1_end and s2_start + 1 == s2_end:
+        return [RawVar(start=s1_start + 1, deleted=s1[s1_start],
+            inserted=s2[s2_start], type="subst")]
 
     # Simple InDel.
-    if s1_start + 1 == s1_end :
-        return [RawVar(start = s1_start + 1, inserted = s2[s2_start:s2_end],
-            type = "delins")]
+    if s1_start + 1 == s1_end:
+        return [RawVar(start=s1_start + 1, inserted=s2[s2_start:s2_end],
+            type="delins")]
 
     # TODO: Refactor the code after this point.
 
@@ -351,14 +338,14 @@ def DNA_description(M, s1, s2, s1_start, s1_end, s2_start, s2_end) :
         lcs_r_len = 0 # s1_end_r and s2_end_r should not be used after this.
 
     # Inversion or Compound variant.
-    default = [RawVar(start = s1_start + 1, end = s1_end,
-        inserted = s2[s2_start:s2_end], type = "delins")]
+    default = [RawVar(start=s1_start + 1, end=s1_end,
+        inserted=s2[s2_start:s2_end], type="delins")]
 
     if not (lcs_f_len or lcs_r_len) : # Optimisation, not really needed.
         return default
 
     # Inversion.
-    if lcs_f_len <= lcs_r_len :
+    if lcs_f_len <= lcs_r_len:
         if trim > 0 : # Partial palindrome.
             s1_end_r -= trim
             s2_end_r -= trim
@@ -366,8 +353,8 @@ def DNA_description(M, s1, s2, s1_start, s1_end, s2_start, s2_end) :
         #if
 
         # Simple Inversion.
-        if s2_end - s2_start == lcs_r_len and s1_end - s1_start == lcs_r_len :
-            return [RawVar(start = s1_start + 1, end = s1_end, type = "inv")]
+        if s2_end - s2_start == lcs_r_len and s1_end - s1_start == lcs_r_len:
+            return [RawVar(start=s1_start + 1, end=s1_end, type="inv")]
 
         r1_len = s1_end_r - lcs_r_len
         r2_len = s1_end - s1_start - s1_end_r
@@ -378,26 +365,26 @@ def DNA_description(M, s1, s2, s1_start, s1_end, s2_start, s2_end) :
         # generate descriptions conditionally.
         leftRv = []
         rightRv = []
-        if r1_len or m2_len :
+        if r1_len or m2_len:
             lcs = len(longest_common_suffix(s1[s1_start:s1_start + r1_len],
                 s2[s2_start:s2_start + m2_len]))
             leftRv = DNA_description(M, s1, s2,
                 s1_start, s1_start + r1_len - lcs,
                 s2_start, s2_start + m2_len - lcs)
         #if
-        if r2_len or m1_len :
+        if r2_len or m1_len:
             lcp = len(longest_common_prefix(s1[s1_end - r2_len:s1_end],
                 s2[s2_end - m1_len:s2_end]))
             rightRv = DNA_description(M, s1, s2,
                 s1_end - r2_len + lcp, s1_end, s2_end - m1_len + lcp, s2_end)
         #if
 
-        partial = leftRv + [RawVar(start = s1_start + r1_len + 1,
-            end = s1_end - r2_len, type = "inv")] + rightRv
+        partial = leftRv + [RawVar(start=s1_start + r1_len + 1,
+            end=s1_end - r2_len, type="inv")] + rightRv
     #if
 
     # Compound variant.
-    else :
+    else:
         r1_len = s1_end_f - lcs_f_len
         r2_len = s1_end - s1_start - s1_end_f
         m1_len = s2_end_f - lcs_f_len
@@ -408,12 +395,12 @@ def DNA_description(M, s1, s2, s1_start, s1_end, s2_start, s2_end) :
             s1_end - r2_len, s1_end, s2_end - m2_len, s2_end)
     #else
 
-    if alleleDescriptionLength(partial) <= alleleDescriptionLength(default) :
+    if alleleDescriptionLength(partial) <= alleleDescriptionLength(default):
         return partial
     return default
 #DNA_description
 
-def describeDNA(original, mutated) :
+def describeDNA(original, mutated):
     """
     Convenience function for DNA_description().
 
@@ -425,7 +412,6 @@ def describeDNA(original, mutated) :
     @returns: A list of RawVar objects, representing the allele.
     @rval: list(RawVar)
     """
-
     s1 = str(original)
     s2 = str(mutated)
     lcp = len(longest_common_prefix(s1, s2))
@@ -435,9 +421,5 @@ def describeDNA(original, mutated) :
 
     M = LCSMatrix(s1, s2)
 
-    description = DNA_description(M, s1, s2, lcp, s1_end, lcp, s2_end)
-    for i in description:
-        i.putHGVS()
-
-    return description
+    return DNA_description(M, s1, s2, lcp, s1_end, lcp, s2_end)
 #describeDNA

mutalyzer/templates/about.html

@@ -8,13 +8,13 @@
         <h3>About</h3>
       </center>
       Mutalyzer <span tal:content = "structure string:${version}"></span>
-      is designed and developed by Jeroen F. J. Laros, with the
+      is designed and developed by Jeroen F.J. Laros, with the
       following exceptions:
       <ul>
         <li>The LRG parser, as well as the Batch interfaces are written
             by Gerben R. Stouten.</li>
         <li>The position converter interfaces (webservice and WWW) are
-            written by Gerard C. P. Schaafsma.</li>
+            written by Gerard C.P. Schaafsma.</li>
         <li>Current development and maintenance is done by Martijn
             Vermaat.</li>
       </ul>
@@ -22,12 +22,12 @@
       valuable work on previous versions that acted as a guideline for the
       development of the current version:
       <ul>
-        <li>Martin Wildeman.</li>
         <li>Ernest van Ophuizen.</li>
+        <li>Martin Wildeman.</li>
         <li>Corinne Bareil.</li>
         <li>Gerben R. Stouten.</li>
       </ul>
-      Specifications are given by Peter E. M. Taschner and Johan T. den
+      Specifications are given by Peter E.M. Taschner and Johan T. den
       Dunnen.<br>
       <br>
       Since references to WWW-sites are not yet acknowledged as citations,