Merging, 12 changed files

Bio/Blast/Applications.py

@@ -24,6 +24,11 @@
 - NcbirpsblastCommandline - Reverse Position Specific BLAST
 - NcbirpstblastnCommandline - Translated Reverse Position Specific BLAST
 
+For further details, see:
+
+Camacho et al. BLAST+: architecture and applications
+BMC Bioinformatics 2009, 10:421
+doi:10.1186/1471-2105-10-421
 """
 from Bio.Application import _Option, AbstractCommandline, _Switch
 
@@ -332,7 +337,7 @@ def __init__(self, cmd="rpsblast",**kwargs):
 
 
 class _NcbiblastCommandline(AbstractCommandline):
-    """Base Commandline object for (classic) NCBI BLAST wrappers (PRIVATE).
+    """Base Commandline object for (new) NCBI BLAST+ wrappers (PRIVATE).
 
     This is provided for subclassing, it deals with shared options
     common to all the BLAST tools (blastn, rpsblast, rpsblast, etc).
@@ -475,7 +480,7 @@ def _validate_incompatibilities(self, incompatibles):
                                          % (a,b))
 
 class _Ncbiblast2SeqCommandline(_NcbiblastCommandline):
-    """Base Commandline object for (classic) NCBI BLAST wrappers (PRIVATE).
+    """Base Commandline object for (new) NCBI BLAST+ wrappers (PRIVATE).
 
     This is provided for subclassing, it deals with shared options
     common to all the BLAST tools supporting two-sequence BLAST
@@ -692,6 +697,13 @@ def __init__(self, cmd="blastn", **kwargs):
                     "Minimum raw gapped score to keep an alignment in the preliminary gapped and traceback stages (integer).", False),
             _Switch(["-ungapped", "ungapped"], ["input"],
                     "Perform ungapped alignment only?"),
+            _Option(["-off_diagonal_range", "off_diagonal_range"], ["input"], None, 0,
+                    """Number of off-diagonals to search for the 2nd hit (integer).
+                    
+                    Expects a positive integer, or 0 (default) to turn off.
+                    
+                    Added in BLAST 2.2.23+
+                    """, False),
             ]
         _Ncbiblast2SeqCommandline.__init__(self, cmd, **kwargs)
 

Bio/Blast/NCBIStandalone.py

@@ -2041,7 +2041,7 @@ def _safe_int(str):
         pass
     # If it fails again, maybe it's too long?
     # XXX why converting to float?
-    return int(float(str))
+    return long(float(str))
 
 def _safe_float(str):
     # Thomas Rosleff Soerensen (rosleff@mpiz-koeln.mpg.de) noted that

Bio/Phylo/PhyloXML.py

@@ -794,7 +794,7 @@ class Point(PhyloElement):
     def __init__(self, geodetic_datum, lat, long, alt=None, alt_unit=None):
         self.geodetic_datum = geodetic_datum
         self.lat = lat
-        self.long = int
+        self.long = long
         self.alt = alt
         self.alt_unit = alt_unit
 

Bio/Prosite/Prodoc.py

@@ -315,7 +315,7 @@ def index_file(filename, indexname, rec2key=None):
     end = 0
     for record in records:
         start = end
-        end = int(handle.tell())
+        end = long(handle.tell())
         length = end - start
 
         if rec2key is not None:

Bio/Prosite/__init__.py

@@ -730,7 +730,7 @@ def index_file(filename, indexname, rec2key=None):
     end = 0
     for record in records:
         start = end
-        end = int(handle.tell())
+        end = long(handle.tell())
         length = end - start
 
         if rec2key is not None:

Bio/SeqIO/InsdcIO.py

@@ -204,7 +204,7 @@ def _write_feature_qualifier(self, key, value=None, quote=None):
         #self.handle.write('%s/%s="%s"\n' % (self.QUALIFIER_INDENT_STR, key, value))
         if quote is None:
             #Try to mimic unwritten rules about when quotes can be left out:
-            if isinstance(value, int) or isinstance(value, int):
+            if isinstance(value, int) or isinstance(value, long):
                 quote = False
             else:
                 quote = True

Bio/SwissProt/SProt.py

@@ -1211,7 +1211,7 @@ def index_file(filename, indexname, rec2key=None):
     end = 0
     for record in records:
         start = end
-        end = int(handle.tell())
+        end = long(handle.tell())
         length = end - start
 
         if rec2key is not None:

BioSQL/Loader.py

@@ -466,7 +466,7 @@ def _get_taxon_id_from_ncbi_lineage(self, taxonomic_lineage):
         if len(taxonomic_lineage) > 1:
             #Use recursion to find out the taxon id (database key) of the parent.
             parent_taxon_id = self._get_taxon_id_from_ncbi_lineage(taxonomic_lineage[:-1])
-            assert isinstance(parent_taxon_id, int) or isinstance(parent_taxon_id, int), repr(parent_taxon_id)
+            assert isinstance(parent_taxon_id, int) or isinstance(parent_taxon_id, long), repr(parent_taxon_id)
         else:
             parent_taxon_id = None
 
@@ -476,7 +476,7 @@ def _get_taxon_id_from_ncbi_lineage(self, taxonomic_lineage):
                 "INSERT INTO taxon(ncbi_taxon_id, parent_taxon_id, node_rank)"\
                 " VALUES (%s, %s, %s)", (ncbi_taxon_id, parent_taxon_id, rank))
         taxon_id = self.adaptor.last_id("taxon")
-        assert isinstance(taxon_id, int) or isinstance(taxon_id, int), repr(taxon_id)
+        assert isinstance(taxon_id, int) or isinstance(taxon_id, long), repr(taxon_id)
         # ... and its name in taxon_name
         scientific_name = taxonomic_lineage[-1].get("ScientificName", None)
         if scientific_name:

Tests/test_NCBI_BLAST_tools.py

@@ -180,14 +180,24 @@ def check(self, exe_name, wrapper) :
         if "-use_test_remote_service" in missing :
             #Known issue, seems to be present in some builds (Bug 3043)
             missing.remove("-use_test_remote_service")
-
-        if extra or missing :
-            raise MissingExternalDependencyError("BLAST+ and Biopython out of sync. "
-                  "Your version of the NCBI BLAST+ tool %s does not match what we "
-                  "are expecting. Please update your copy of Biopython, or report "
-                  "this issue if you are already using the latest version. "
-                  "(Exta args: %s; Missing: %s)" \
-                  % (exe_name, ",".join(sorted(extra)), ",".join(sorted(missing))))
+        if exe_name == "blastn" and "-off_diagonal_range" in extra:
+            #Added in BLAST 2.2.23+
+            extra.remove("-off_diagonal_range")
+        if exe_name == "tblastx":
+            #These appear to have been removed in BLAST 2.2.23+
+            #(which seems a bit odd - TODO - check with NCBI?)
+            extra = extra.difference(["-gapextend","-gapopen",
+                                      "-xdrop_gap","-xdrop_gap_final"])
+
+        if extra or missing:
+            raise MissingExternalDependencyError("BLAST+ and Biopython out "
+                  "of sync. Your version of the NCBI BLAST+ tool %s does not "
+                  "match what we are expecting. Please update your copy of "
+                  "Biopython, or report this issue if you are already using "
+                  "the latest version. (Exta args: %s; Missing: %s)" \
+                  % (exe_name,
+                     ",".join(sorted(extra)),
+                     ",".join(sorted(missing))))
 
         #An almost trivial example to test any validation
         cline = wrapper(exe, query="dummy")

Tests/test_PDB.py

@@ -15,24 +15,16 @@
 from io import StringIO
 
 try:
-    from numpy.random import random
+    import numpy
 except ImportError:
     from Bio import MissingExternalDependencyError
     raise MissingExternalDependencyError(\
         "Install NumPy if you want to use Bio.PDB.")
 
-try:
-    from Bio.KDTree import _CKDTree
-except ImportError:
-    from Bio import MissingExternalDependencyError
-    raise MissingExternalDependencyError(\
-        "C module in Bio.KDTree not compiled")
-
 from Bio.Seq import Seq
 from Bio.Alphabet import generic_protein
 from Bio.PDB import PDBParser, PPBuilder, CaPPBuilder, PDBIO
 from Bio.PDB import HSExposureCA, HSExposureCB, ExposureCN
-from Bio.PDB.NeighborSearch import NeighborSearch
 from Bio.PDB.PDBExceptions import PDBConstructionException, PDBConstructionWarning
 
 
@@ -693,27 +685,6 @@ def test_ExposureCN(self):
         self.assertEqual(1, len(residues[-1].xtra))
         self.assertEqual(38, residues[-1].xtra["EXP_CN"])
 
-
-class NeighborTest(unittest.TestCase):
-    def setUp(self):
-        warnings.resetwarnings()
-
-    def test_neighbor_search(self):
-        """NeighborSearch: Find nearby randomly generated coordinates.
-         
-        Based on the self test in Bio.PDB.NeighborSearch.
-        """
-        class RandomAtom:
-            def __init__(self):
-                self.coord = 100 * random(3)
-            def get_coord(self):
-                return self.coord
-        for i in range(0, 20):
-            atoms = [RandomAtom() for j in range(100)]
-            ns = NeighborSearch(atoms)
-            hits = ns.search_all(5.0)
-            self.assertTrue(hits >= 0)
-
 # -------------------------------------------------------------
 
 if __name__ == '__main__':

Tests/test_PDB_KDTree.py

@@ -0,0 +1,49 @@
+# Copyright 2009-2010 by Eric Talevich.  All rights reserved.
+# Revisions copyright 2010 by Peter Cock.  All rights reserved.
+#
+# Converted by Eric Talevich from an older unit test copyright 2002
+# by Thomas Hamelryck.
+# 
+# This code is part of the Biopython distribution and governed by its
+# license. Please see the LICENSE file that should have been included
+# as part of this package.
+
+"""Unit tests for those parts of the Bio.PDB module using Bio.KDTree."""
+import unittest
+
+try:
+    from numpy.random import random
+except ImportError:
+    from Bio import MissingExternalDependencyError
+    raise MissingExternalDependencyError(\
+        "Install NumPy if you want to use Bio.PDB.")
+
+try:
+    from Bio.KDTree import _CKDTree
+except ImportError:
+    from Bio import MissingExternalDependencyError
+    raise MissingExternalDependencyError(\
+        "C module in Bio.KDTree not compiled")
+
+from Bio.PDB.NeighborSearch import NeighborSearch
+
+class NeighborTest(unittest.TestCase):
+    def test_neighbor_search(self):
+        """NeighborSearch: Find nearby randomly generated coordinates.
+         
+        Based on the self test in Bio.PDB.NeighborSearch.
+        """
+        class RandomAtom:
+            def __init__(self):
+                self.coord = 100 * random(3)
+            def get_coord(self):
+                return self.coord
+        for i in range(0, 20):
+            atoms = [RandomAtom() for j in range(100)]
+            ns = NeighborSearch(atoms)
+            hits = ns.search_all(5.0)
+            self.assertTrue(hits >= 0)
+
+if __name__ == '__main__':
+    runner = unittest.TextTestRunner(verbosity=2)
+    unittest.main(testRunner=runner)

setup.py

@@ -138,7 +138,8 @@ def run(self):
         if not check_dependencies_once():
             return
         # add software that requires NumPy to install
-        if is_Numpy_installed():
+        # TODO - Convert these for Python 3
+        if is_Numpy_installed() and sys.version_info[0] < 3:
             import numpy
             numpy_include_dir = numpy.get_include()
             self.extensions.append(