minor

seqdata.py

@@ -661,11 +661,13 @@ class BedFile():
                     newrows.append(entry)
         return BedFile(newrows, format = self.format)
         
-    def write(self, filename, format = 'BED6'):
+    def write(self, filename, format = 'BED6', header = None):
         """ Save the data
             format - the format to use for WRITING, currently only BED6 ('Optional' 6-col format) is supported.
         """
         f = open(filename, 'w')
+        if header:
+            f.write(header + '\n')
         for row in self.__iter__():
             if self.format == 'Peaks':
                 #f.write("%s %d %d %s %d %s %f %f" % (row.chrom, row.chromStart, row.chromEnd, row.name, row.score, row.strand, row.signalValue, row.pValue)) # seems to cause issues in UCSD Genome Browser
@@ -713,11 +715,13 @@ def readBedFile(filename, format = 'Limited'):
     """
     return BedFile(filename, format)
     
-def writeBedFile(entries, filename, format = 'BED6'):
+def writeBedFile(entries, filename, format = 'BED6', header = None):
     """ Save the BED entries to a BED file.
         format - the format to use for WRITING, currently only BED6 ('Optional' 6-col format) is supported.
     """
     f = open(filename, 'w')
+    if header:
+        f.write(header + '\n')
     for row in entries:
         if format == 'Peaks':
             #f.write("%s %d %d %s %d %s %f %f" % (row.chrom, row.chromStart, row.chromEnd, row.name, row.score, row.strand, row.signalValue, row.pValue)) # seems to cause issues in UCSD Genome Browser