[pygr-notify] [pygr commit] r127 - code-reviews/seqdb-review

[codesite-noreply at google.com]

Author: istvan.albert
Date: Wed Jan 21 05:58:20 2009
New Revision: 127

Modified:
    code-reviews/seqdb-review/seqdb.py

Log:
code review candidate test

Modified: code-reviews/seqdb-review/seqdb.py
==============================================================================
--- code-reviews/seqdb-review/seqdb.py	(original)
+++ code-reviews/seqdb-review/seqdb.py	Wed Jan 21 05:58:20 2009
@@ -1,8 +1,8 @@
  from __future__ import generators
-import os
+import os, sys
  from sequence import *
  from sqlgraph import *
-import classutil
+import classutil, logger
  import UserDict
  import weakref
  from annotation import AnnotationDB, AnnotationSeq, AnnotationSlice, \
@@ -24,7 +24,7 @@
      def strslice(self,start,end):
          "Efficient access to slice of a sequence, useful for huge contigs"
          return self._select('substring(%s FROM %d FOR %d)'
-                            %(self.db._attrSQL('seq'),start+1,end-start))
+                            %(self.db._attrSQL('sequence'),start+1,end-start))

  class DNASQLSequence(SQLSequence):
      _seqtype=DNA_SEQTYPE
@@ -76,41 +76,39 @@
          finally:
              ifile2.close()

-def store_seqlen_dict(d, filename, ifile=None, idFilter=None, reader=None):
+def store_seqlen_dict(d, filename=None, stream=None, idFilter=None,  
reader=None):
      "store sequence lengths in a dictionary"
-    if reader is not None: # run the user's custom reader() function.
-        builder = SeqLenDictSaver(reader)
-    else:
-        try: # TRY TO USE OUR FAST COMPILED PARSER
-            import seqfmt
-            builder = seqfmt.read_fasta_lengths
-        except ImportError:
-            import sys
-            raise ImportError('''
-Unable to import extension module pygr.seqfmt that should be part of this  
package.
-Either you are working with an incomplete install, or an installation of  
pygr
-compiled with an incompatible Python version.  Please check your PYTHONPATH
-setting and make sure it is compatible with this Python version (%d.%d).
-When in doubt, rebuild your pygr installation using the
-python setup.py build --force
-option to force a clean install''' % sys.version_info[:2])
-    if idFilter is not None: # need to wrap seqlendict to apply filter...
-        class dictwrapper(object):
+
+    # sanity check
+    assert bool(stream) ^ bool(filename), "Only one  
of 'filename', 'stream' \
+        parameters may be present"
+
+    # apply custom reader() function
+    if reader:
+        builder = SeqLenDictSaver(reader)
+    else:
+        import seqfmt
+        builder = seqfmt.read_fasta_lengths
+
+    # need to wrap seqlendict to apply filter...
+    if idFilter:
+        class DictWrapper(object):
              def __init__(self, idFilter, d):
                  self.d = d
                  self.idFilter = idFilter
              def __setitem__(self, k, v):
                  id = self.idFilter(k)
                  self.d[id] = v
-        d = dictwrapper(idFilter, d) # force builder to write to wrapper...
-    if ifile is not None:
-        builder(d, ifile, filename) # run the builder on our sequence set
-    else:
-        ifile = file(filename)
-        try:
-            builder(d, ifile, filename) # run the builder on our sequence  
set
-        finally:
-            ifile.close()
+        # wrap the dictionary
+        d = DictWrapper(idFilter=idFilter, d=d)
+
+    currstream = stream or file( filename )
+    try:
+        builder(d, currstream, filename) # run the builder on our sequence
+    finally:
+        # close the stream if it was opened here
+        if not stream:
+            currstream.close()

  class FileDBSeqDescriptor(object):
      "Get sequence from a concatenated pureseq database for obj.id"
@@ -134,8 +132,7 @@
              db.seqLenDict = classutil.open_shelve(filepath+'.seqlen','r')  
# READ-ONLY
          except NoSuchFileError: # BUILD: READ ALL SEQ LENGTHS, STORE IN  
PERSIST DICT
              db.seqLenDict = classutil.open_shelve(filepath+'.seqlen','n')  
# NEW EMPTY FILE
-            import sys
-            print >>sys.stderr,'Building sequence length index...'
+            logger.debug( 'building sequence indices' )
              store_seqlen_dict(db.seqLenDict, filepath, **kwargs)
              db.seqLenDict.close() # FORCE IT TO WRITE DATA TO DISK
              db.seqLenDict = classutil.open_shelve(filepath+'.seqlen','r')  
# READ-ONLY