Replace remaining python2-style print commands by python3-style print…

… function (biopython#3533)

* updated print function

* one more

Bio/Align/AlignInfo.py

@@ -367,7 +367,7 @@ def information_content(
                 e_freq_table,
                 random_expected,
             )
-            # print freq_dict,
+            # print(freq_dict, end="")
             column_score = self._get_column_info_content(
                 freq_dict, e_freq_table, log_base, random_expected
             )

Bio/AlignIO/EmbossIO.py

@@ -175,7 +175,7 @@ def __next__(self):
                         index = 0
                 else:
                     # just a start value, this is just alignment annotation (?)
-                    # print "Skipping: " + line.rstrip()
+                    # print("Skipping: " + line.rstrip())
                     pass
             elif line.strip() == "":
                 # Just a spacer?

Bio/AlignIO/Interfaces.py

@@ -61,10 +61,10 @@ def __iter__(self):
 
             with open("many.phy","r") as myFile:
                 for alignment in PhylipIterator(myFile):
-                    print "New alignment:"
+                    print("New alignment:")
                     for record in alignment:
-                        print record.id
-                        print record.seq
+                        print(record.id)
+                        print(record.seq)
 
         """
         return iter(self.__next__, None)

Bio/AlignIO/PhylipIO.py

@@ -247,7 +247,7 @@ def __next__(self):
                 self._header = line
                 break
 
-            # print "New block..."
+            # print("New block...")
             for i in range(number_of_seqs):
                 s = line.strip().replace(" ", "")
                 if "." in s:

Bio/Blast/NCBIWWW.py

@@ -323,7 +323,7 @@ def _parse_qblast_ref_page(handle):
             msg = s[i:].split("<", 1)[0].split("\n", 1)[0].strip()
             raise ValueError("Error message from NCBI: %s" % msg)
         # We didn't recognise the error layout :(
-        # print s
+        # print(s)
         raise ValueError(
             "No RID and no RTOE found in the 'please wait' page, "
             "there was probably an error in your request but we "

Bio/Data/CodonTable.py

@@ -312,7 +312,7 @@ def list_ambiguous_codons(codons, ambiguous_nucleotide_values):
                 if codon not in candidates and codon not in codons:
                     candidates.append(codon)
     answer = codons[:]  # copy
-    # print "Have %i new candidates" % len(candidates)
+    # print("Have %i new candidates" % len(candidates))
     for ambig_codon in candidates:
         wanted = True
         # e.g. 'TRR' -> 'TAA', 'TAG', 'TGA', 'TGG'
@@ -325,7 +325,7 @@ def list_ambiguous_codons(codons, ambiguous_nucleotide_values):
             if codon not in codons:
                 # This ambiguous codon can code for a non-stop, exclude it!
                 wanted = False
-                # print "Rejecting %s" % ambig_codon
+                # print("Rejecting %s" % ambig_codon)
                 continue
         if wanted:
             answer.append(ambig_codon)

Bio/Graphics/GenomeDiagram/_CircularDrawer.py

@@ -257,7 +257,7 @@ def draw_track(self, track):
 
     def draw_feature_set(self, set):
         """Return list of feature elements and list of labels for them."""
-        # print 'draw feature set'
+        # print('draw feature set')
         feature_elements = []  # Holds diagram elements belonging to the features
         label_elements = []  # Holds diagram elements belonging to feature labels
 
@@ -420,8 +420,8 @@ def get_feature_sigil(self, feature, locstart, locend, **kwargs):
             # No label required
             labelgroup = None
         # if locstart > locend:
-        #    print locstart, locend, feature.strand, sigil, feature.name
-        # print locstart, locend, feature.name
+        #    print(locstart, locend, feature.strand, sigil, feature.name)
+        # print(locstart, locend, feature.name)
         return sigil, labelgroup
 
     def draw_cross_link(self, cross_link):
@@ -522,7 +522,7 @@ def draw_graph_set(self, set):
          - set       GraphSet object
 
         """
-        # print 'draw graph set'
+        # print('draw graph set')
         elements = []  # Holds graph elements
 
         # Distribution dictionary for how to draw the graph
@@ -1176,7 +1176,7 @@ def _draw_arc_line(
                 a = (
                     (start_angle + x * (angle_diff)) * pi / 180
                 )  # to radians for sin/cos
-                # print x0+r*cos(a), y0+r*sin(a)
+                # print(x0+r*cos(a), y0+r*sin(a))
                 path.lineTo(x0 + r * cos(a), y0 + r * sin(a))
                 x += dx
         a = end_angle * pi / 180

Bio/Graphics/GenomeDiagram/_Graph.py

@@ -130,7 +130,7 @@ def range(self):
         """
         positions = sorted(self.data)  # i.e. dict keys
         # Return first and last positions in graph
-        # print len(self.data)
+        # print(len(self.data))
         return (positions[0], positions[-1])
 
     def mean(self):

Bio/Graphics/GenomeDiagram/_LinearDrawer.py

@@ -670,7 +670,7 @@ def draw_feature_set(self, set):
         Returns a tuple (list of elements describing features, list of
         labels for elements).
         """
-        # print 'draw feature set'
+        # print("draw feature set")
         feature_elements = []  # Holds diagram elements belonging to the features
         label_elements = []  # Holds diagram elements belonging to feature labels
 
@@ -721,17 +721,17 @@ def draw_feature_location(self, feature, locstart, locend):
         # Get start and end positions for feature/subfeatures
         start_fragment, start_offset = self.canvas_location(locstart)
         end_fragment, end_offset = self.canvas_location(locend)
-        # print "start_fragment, start_offset", start_fragment, start_offset
-        # print "end_fragment, end_offset", end_fragment, end_offset
-        # print "start, end", locstart, locend
+        # print("start_fragment, start_offset", start_fragment, start_offset)
+        # print("end_fragment, end_offset", end_fragment, end_offset)
+        # print("start, end", locstart, locend)
 
         # Note that there is a strange situation where a feature may be in
         # several parts, and one or more of those parts may end up being
         # drawn on a non-existent fragment.  So we check that the start and
         # end fragments do actually exist in terms of the drawing
         allowed_fragments = list(self.fragment_limits.keys())
         if start_fragment in allowed_fragments and end_fragment in allowed_fragments:
-            # print feature.name, feature.start, feature.end, start_offset, end_offset
+            # print(feature.name, feature.start, feature.end, start_offset, end_offset)
             if start_fragment == end_fragment:  # Feature is found on one fragment
                 feature_box, label = self.get_feature_sigil(
                     feature, start_offset, end_offset, start_fragment
@@ -746,7 +746,7 @@ def draw_feature_location(self, feature, locstart, locend):
                 # The bit that runs up to the end of the first fragment,
                 # and any bits that subsequently span whole fragments
                 while self.fragment_limits[fragment][1] < locend:
-                    # print fragment, self.fragment_limits[fragment][1], locend
+                    # print(fragment, self.fragment_limits[fragment][1], locend)
                     feature_box, label = self.get_feature_sigil(
                         feature, start, self.pagewidth, fragment
                     )
@@ -758,14 +758,14 @@ def draw_feature_location(self, feature, locstart, locend):
                     # if label is not None:   # There's a label for the feature
                     #    label_elements.append(label)
                 # The last bit of the feature
-                # print locend, self.end, fragment
-                # print self.fragment_bases, self.length
+                # print(locend, self.end, fragment)
+                # print(self.fragment_bases, self.length)
                 feature_box, label = self.get_feature_sigil(
                     feature, 0, end_offset, fragment
                 )
                 feature_boxes.append((feature_box, label))
         # if locstart > locend:
-        #    print locstart, locend, feature.strand, feature_boxes, feature.name
+        #    print(locstart, locend, feature.strand, feature_boxes, feature.name)
         return feature_boxes
 
     def draw_cross_link(self, cross_link):
@@ -1169,7 +1169,7 @@ def draw_graph_set(self, set):
 
         Returns tuple (list of graph elements, list of graph labels).
         """
-        # print 'draw graph set'
+        # print('draw graph set')
         elements = []  # Holds graph elements
 
         # Distribution dictionary for how to draw the graph
@@ -1191,7 +1191,7 @@ def draw_line_graph(self, graph):
          - graph     Graph object
 
         """
-        # print '\tdraw_line_graph'
+        # print('\tdraw_line_graph')
         line_elements = []  # Holds drawable elements
 
         # Get graph data
@@ -1284,7 +1284,7 @@ def draw_line_graph(self, graph):
 
     def draw_heat_graph(self, graph):
         """Return a list of drawable elements for the heat graph."""
-        # print '\tdraw_heat_graph'
+        # print('\tdraw_heat_graph')
         # At each point contained in the graph data, we draw a box that is the
         # full height of the track, extending from the midpoint between the
         # previous and current data points to the midpoint between the current
@@ -1312,7 +1312,7 @@ def draw_heat_graph(self, graph):
             fragment0, x0 = self.canvas_location(pos0)
             fragment1, x1 = self.canvas_location(pos1)
             x0, x1 = self.x0 + x0, self.x0 + x1  # account for margin
-            # print 'x1 before:', x1
+            # print('x1 before:', x1)
 
             # Calculate the heat color, based on the differential between
             # the value and the median value
@@ -1326,8 +1326,8 @@ def draw_heat_graph(self, graph):
                     x1 = self.xlim
                 ttop = top + self.fragment_lines[fragment0][0]
                 tbtm = btm + self.fragment_lines[fragment0][0]
-                # print 'equal', pos0, pos1, val
-                # print pos0, pos1, fragment0, fragment1
+                # print('equal', pos0, pos1, val)
+                # print(pos0, pos1, fragment0, fragment1)
                 heat_elements.append(
                     draw_box((x0, tbtm), (x1, ttop), color=heat, border=None)
                 )
@@ -1337,7 +1337,7 @@ def draw_heat_graph(self, graph):
                 fragment = fragment0
                 start_x = x0
                 while self.fragment_limits[fragment][1] <= pos1:
-                    # print pos0, self.fragment_limits[fragment][1], pos1
+                    # print(pos0, self.fragment_limits[fragment][1], pos1)
                     ttop = top + self.fragment_lines[fragment][0]
                     tbtm = btm + self.fragment_lines[fragment][0]
                     heat_elements.append(
@@ -1350,7 +1350,7 @@ def draw_heat_graph(self, graph):
                 ttop = top + self.fragment_lines[fragment][0]
                 tbtm = btm + self.fragment_lines[fragment][0]
                 # Add the last part of the bar
-                # print 'x1 after:', x1, '\n'
+                # print('x1 after:', x1, '\n')
                 heat_elements.append(
                     draw_box((self.x0, tbtm), (x1, ttop), color=heat, border=None)
                 )
@@ -1359,7 +1359,7 @@ def draw_heat_graph(self, graph):
 
     def draw_bar_graph(self, graph):
         """Return list of drawable elements for a bar graph."""
-        # print '\tdraw_bar_graph'
+        # print('\tdraw_bar_graph')
         # At each point contained in the graph data, we draw a vertical bar
         # from the track center to the height of the datapoint value (positive
         # values go up in one color, negative go down in the alternative

Bio/Nexus/Nexus.py

@@ -997,7 +997,7 @@ def _charstatelabels(self, options):
 
     def _statelabels(self, options):
         # self.charlabels = options
-        # print 'Command statelabels is not supported and will be ignored.'
+        # print("Command statelabels is not supported and will be ignored.")
         pass
 
     def _matrix(self, options):
@@ -1855,9 +1855,9 @@ def constant(self, matrix=None, delete=(), exclude=()):
         for taxon in undelete[1:]:
             newconstant = []
             for site in constant:
-                # print '%d (paup=%d)' % (site[0],site[0]+1),
+                # print("%d (paup=%d)" % (site[0],site[0]+1), end="")
                 seqsite = matrix[taxon][site[0]].upper()
-                # print seqsite,'checked against',site[1],'\t',
+                # print(seqsite,"checked against",site[1],"\t", end="")
                 if (
                     seqsite == self.missing
                     or (
@@ -1887,11 +1887,11 @@ def constant(self, matrix=None, delete=(), exclude=()):
                     )
                     if intersect:
                         newconstant.append((site[0], "".join(intersect)))
-                    #    print 'ok'
+                    #    print("ok")
                     # else:
-                    #    print 'failed'
+                    #    print("failed")
                 # else:
-                #    print 'failed'
+                #    print("failed")
             constant = newconstant
         cpos = [s[0] for s in constant]
         return cpos
@@ -1996,7 +1996,7 @@ def add_sequence(self, name, sequence):
 
         if name in self.taxlabels:
             unique_name = _unique_label(self.taxlabels, name)
-            # print "WARNING: Sequence name %s is already present. Sequence was added as %s." % (name,unique_name)
+            # print("WARNING: Sequence name %s is already present. Sequence was added as %s." % (name,unique_name))
         else:
             unique_name = name
 

Bio/SearchIO/_legacy/NCBIStandalone.py

@@ -1778,11 +1778,11 @@ def __next__(self):
 
         if query and "BLAST" not in lines[0]:
             # Cheat and re-insert the header
-            # print "-"*50
-            # print "".join(self._header)
-            # print "-"*50
-            # print "".join(lines)
-            # print "-"*50
+            # print("-"*50)
+            # print("".join(self._header))
+            # print("-"*50)
+            # print("".join(lines))
+            # print("-"*50)
             lines = self._header + lines
 
         if not lines:

Bio/motifs/jaspar/db.py

@@ -729,7 +729,7 @@ def _fetch_internal_id_list(
         if where_clauses:
             sql = "".join([sql, " where ", " and ".join(where_clauses)])
 
-        # print "sql = %s" % sql
+        # print("sql = %s" % sql)
 
         cur.execute(sql)
         rows = cur.fetchall()

BioSQL/Loader.py

@@ -650,8 +650,8 @@ def _load_bioentry_table(self, record):
          %s,
          %s,
          %s)"""
-        # print self.dbid, taxon_id, record.name, accession, identifier, \
-        #        division, description, version
+        # print(self.dbid, taxon_id, record.name, accession, identifier, \
+        #        division, description, version)
         self.adaptor.execute(
             sql,
             (
@@ -795,8 +795,8 @@ def _load_annotations(self, record, bioentry_id):
                 self.adaptor.execute(mono_sql, (bioentry_id, term_id, str(value)))
             else:
                 pass
-                # print "Ignoring annotation '%s' entry of type '%s'" \
-                #      % (key, type(value))
+                # print("Ignoring annotation '%s' entry of type '%s'" \
+                #      % (key, type(value)))
 
     def _load_reference(self, reference, rank, bioentry_id):
         """Record SeqRecord's annotated references in the database (PRIVATE).

Tests/test_codonalign.py

@@ -173,7 +173,7 @@ def setUp(self):
 
     def test_IO(self):
         self.assertEqual(len(self.alns), 6)
-        # print temp_dir
+        # print(temp_dir)
         for n, i in enumerate(self.alns):
             aln = i.toMultipleSeqAlignment()
             AlignIO.write(aln, temp_dir + "/aln" + str(n) + ".clw", "clustal")