@@ -23,7 +23,7 @@ Iterator Iterate through a number of compass records """ from Bio import File from Bio.ParserSupport import * -import re,string +import re class Record: """ @@ -54,12 +54,12 @@ class Record: def query_coverage(self): """Return the length of the query covered in alignment""" - s = string.replace(self.query_aln, "=", "") + s = self.query_aln.replace("=", "") return len(s) def hit_coverage(self): """Return the length of the hit covered in the alignment""" - s = string.replace(self.hit_aln, "=", "") + s = self.hit_aln.replace("=", "") return len(s) class _Scanner: @@ -255,6 +255,6 @@ class Iterator: if not lines: return None - data = string.join(lines, '') + data = ''.join(lines) return self._parser.parse(File.StringHandle(data)) Bio/Compass/__init__.py 5b87d6f3787d3dc107db430d3071a82751e9f511 mdehoon mdehoon http://github.com/etal/biopython/commit/8d4fc3bbfc5ef6105efba47173a8d7571ef8d6b9 8d4fc3bbfc5ef6105efba47173a8d7571ef8d6b9 2008-11-26T20:28:50-08:00 2008-11-26T20:28:50-08:00 Removing deprecated string functions. See bug #2688. d27aecc8787e6e170c414817ca68f37495a70e6b mdehoon mdehoon