[Biopython-dev] [Bug 2957] New: GenBank Writer Should Write Out Date

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Mon Nov 30 19:06:12 UTC 2009


           Summary: GenBank Writer Should Write Out Date
           Product: Biopython
           Version: 1.52
          Platform: PC
        OS/Version: Windows
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: n.j.loman at bham.ac.uk


Would it be possible to modify the GenBank writer to output the date in the
LOCUS header. When reading GenBank files this is already parsed in the correct
format into record.annotations, so the following patch would work:

 diff -u InsdcIO.py InsdcIO-date.py
--- InsdcIO.py  2009-11-30 19:54:05.000000000 +0000
+++ InsdcIO-date.py     2009-11-30 19:55:32.000000000 +0000
@@ -278,12 +278,13 @@
         assert len(division) == 3
         #TODO - date
         #TODO - mol_type
-        line = "LOCUS       %s %s %s    %s           %s 01-JAN-1980\n" \
+        line = "LOCUS       %s %s %s    %s           %s %s\n" \
                      % (locus.ljust(16),
-                        division)
+                        division,
+                        record.annotations.get('date', '01-JAN-1980'))
         assert len(line) == 79+1, repr(line) #plus one for new line

         assert line[12:28].rstrip() == locus, \

I realise you might not work when converting between different record types,
but this would suit my needs for the time being. 


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