[Biopython-dev] Biopython SwissProt bugs

[Brad Chapman]

Hi OEyvind;

(My sincerest apologies if I'm mangling your first name)

Thanks for the bug reports for SwissProt (bugs 23 and 24 for those on
the dev list). I fixed both of the problems, and have attached patches 
against the latest CVS version (which should also work with the latest 
release 1.00a1). I'm not positive if they will apply cleanly to
0.90d04, but that might be a good excuse for you to upgrade to the
most recent release :-).

For the RX line problem, it looks to me like SwissProt now uses RX
lines like:

RX   PubMed=9603189;

in some places, where I guess they used to be:

RX   MEDLINE; 85132727.

This confused the parser, so I fixed it to check for and handle these
new cases.

For the second problem with the extra spaces in VARSPLIC lines, I just 
added a special case to check for this and correct it.

These seem to work for me on the examples you provided -- if you could 
confirm that they work for you, that would be super.

I'm sending the patch to the dev list so Jeff, the master o' SwissProt,
can look it over before I check the changes and added tests into CVS.

Thanks again for the bug reports.

Brad

-------------- next part --------------
*** SProt.py.orig	Sun Mar 11 16:01:22 2001
--- SProt.py	Sun Mar 11 17:14:53 2001
***************
*** 590,595 ****
--- 590,598 ----
      
      def reference_cross_reference(self, line):
          assert self.data.references, "RX: missing RN"
+         # The basic (older?) RX line is of the form:
+         # RX   MEDLINE; 85132727.
+         # but there are variants of this that need to be dealt with (see below)
          
          # CLD1_HUMAN in Release 39 and DADR_DIDMA in Release 33
          # have extraneous information in the RX line.  Check for
***************
*** 599,609 ****
          if ind >= 0:
              line = line[:ind]
  
!         cols = string.split(line)
!         assert len(cols) == 3, "I don't understand RX line %s" \
!                % line
!         self.data.references[-1].references.append(
!             (self._chomp(cols[1]), self._chomp(cols[2])))
      
      def reference_author(self, line):
          assert self.data.references, "RA: missing RN"
--- 602,634 ----
          if ind >= 0:
              line = line[:ind]
  
!         # RX lines can also be used of the form
!         # RX   PubMed=9603189;
!         # reported by edvard at farmasi.uit.no
!         # and these can be more complicated like:
!         # RX   MEDLINE=95385798; PubMed=7656980;
!         # We look for these cases first and deal with them
!         if string.find(line, "=") != -1:
!             cols = string.split(line)
!             assert len(cols) > 1, "I don't understand RX line %s" % line
! 
!             for info_col in cols[1:]:
!                 id_cols = string.split(info_col, "=")
!                 if len(id_cols) == 2:
!                     self.data.references[-1].references.append(
!                         (self._chomp(id_cols[0]), self._chomp(id_cols[1])))
!                 else:
!                     raise AssertionError("I don't understand RX line %s"
!                                          % line)
!         # otherwise we assume we have the type 'RX   MEDLINE; 85132727.'
!         else:
!             cols = string.split(line)
!             # normally we split into the three parts
!             if len(cols) == 3:
!                 self.data.references[-1].references.append(
!                     (self._chomp(cols[1]), self._chomp(cols[2])))
!             else:
!                 raise AssertionError("I don't understand RX line %s" % line)
      
      def reference_author(self, line):
          assert self.data.references, "RA: missing RN"
***************
*** 677,683 ****
--- 702,741 ----
              name, from_res, to_res, old_description = self.data.features[-1]
              del self.data.features[-1]
              description = "%s %s" % (old_description, description)
+             
+             # special case -- VARSPLIC, reported by edvard at farmasi.uit.no
+             if name == "VARSPLIC":
+                 description = self._fix_varsplic_sequences(description)
          self.data.features.append((name, from_res, to_res, description))
+ 
+     def _fix_varsplic_sequences(self, description):
+         """Remove unwanted spaces in sequences.
+ 
+         During line carryover, the sequences in VARSPLIC can get mangled
+         with unwanted spaces like:
+         'DISSTKLQALPSHGLESIQT -> PCRATGWSPFRRSSPC LPTH'
+         We want to check for this case and correct it as it happens.
+         """
+         descr_cols = string.split(description, " -> ")
+         if len(descr_cols) == 2:
+             first_seq = descr_cols[0]
+             second_seq = descr_cols[1]
+             extra_info = ''
+             # we might have more information at the end of the
+             # second sequence, which should be in parenthesis
+             extra_info_pos = string.find(second_seq, " (")
+             if extra_info_pos != -1:
+                 extra_info = second_seq[extra_info_pos:]
+                 second_seq = second_seq[:extra_info_pos]
+ 
+             # now clean spaces out of the first and second string
+             first_seq = string.replace(first_seq, " ", "")
+             second_seq = string.replace(second_seq, " ", "")
+ 
+             # reassemble the description
+             description = first_seq + " -> " + second_seq + extra_info
+ 
+         return description
      
      def sequence_header(self, line):
          cols = string.split(line)