remove spurious print statements (#4198)

* remove spurious print statements

* remove unneeded import

* add comment

Bio/Align/__init__.py

@@ -2623,8 +2623,8 @@ class Alignment:
         to a sort value.  For example, you could sort on the GC content of each
         sequence.
 
-        >>> from Bio.SeqUtils import GC
-        >>> alignment.sort(key=GC)
+        >>> from Bio.SeqUtils import gc_fraction
+        >>> alignment.sort(key=gc_fraction)
         >>> print(alignment)
         target            0 AATAA 5
                           0 ||.|| 5
@@ -2633,7 +2633,7 @@ class Alignment:
 
         You can reverse the sort order by passing `reverse=True`:
 
-        >>> alignment.sort(key=GC, reverse=True)
+        >>> alignment.sort(key=gc_fraction, reverse=True)
         >>> print(alignment)
         target            0 AAGAA 5
                           0 ||.|| 5

Bio/Align/clustal.py

@@ -247,8 +247,6 @@ class AlignmentIterator(interfaces.AlignmentIterator):
         if consensus:
             rows, columns = alignment.shape
             if len(consensus) != columns:
-                for aligned_seq in aligned_seqs:
-                    print(aligned_seq, len(aligned_seq))
                 raise ValueError(
                     "Alignment has %i columns, consensus length is %i, '%s'"
                     % (columns, len(consensus), consensus)

Bio/ExPASy/cellosaurus.py

@@ -18,20 +18,30 @@ Classes:
 
 Examples
 --------
-You need to download the Cellosaurus database for this examples to
-run, e.g. from ftp://ftp.expasy.org/databases/cellosaurus/cellosaurus.txt
+This example downloads the Cellosaurus database and parses it. Note that
+urlopen returns a stream of bytes, while the parser expects a stream of plain
+string, so we use TextIOWrapper to convert bytes to string using the UTF-8
+encoding. This is not needed if you download the cellosaurus.txt file in
+advance and open it (see the comment below).
 
-    >> from Bio.ExPASy import cellosaurus
-    >> with open('cellosaurus.txt') as handle:
-    ...    records = cellosaurus.parse(handle)
-    ...    for record in records:
-    ...        if 'Homo sapiens' in record['OX'][0]:
-    ...            print(record['ID'])
+    >>> from urllib.request import urlopen
+    >>> from io import TextIOWrapper
+    >>> from Bio.ExPASy import cellosaurus
+    >>> url = "ftp://ftp.expasy.org/databases/cellosaurus/cellosaurus.txt"
+    >>> bytestream = urlopen(url)
+    >>> textstream = TextIOWrapper(bytestream, "UTF-8")
+    >>> # alternatively, use
+    >>> # textstream = open("cellosaurus.txt")
+    >>> # if you downloaded the cellosaurus.txt file in advance.
+    >>> records = cellosaurus.parse(textstream)
+    >>> for record in records:
+    ...     if 'Homo sapiens' in record['OX'][0]:
+    ...         print(record['ID'])  # doctest:+ELLIPSIS
     ...
     #15310-LN
     #W7079
     (L)PC6
-    00136
+    0.5alpha
     ...
 
 """
@@ -188,3 +198,9 @@ def __read(handle):
                 continue
     if record:
         raise ValueError("Unexpected end of stream")
+
+
+if __name__ == "__main__":
+    from Bio._utils import run_doctest
+
+    run_doctest()

Bio/Geo/Record.py

@@ -55,9 +55,7 @@ class Record:
                 output += f"{key}: {contents[:40]}\n"
                 output += out_block(contents[40:])
             else:
-                print(contents)
-                output += f"{key}: {contents[:40]}\n"
-                output += out_block(contents[40:])
+                raise RuntimeError(f"unexpected contents of type {type(contents)}")
         col_keys = sorted(self.col_defs)
         output += "Column Header Definitions\n"
         for key in col_keys:

Bio/Medline/__init__.py

@@ -210,3 +210,9 @@ def read(handle):
     """
     records = parse(handle)
     return next(records)
+
+
+if __name__ == "__main__":
+    from Bio._utils import run_doctest
+
+    run_doctest()

Bio/Nexus/Nexus.py

@@ -707,7 +707,6 @@ class Nexus:
                 file_contents = input
                 self.filename = "input_string"
             else:
-                print(input.strip()[:50])
                 raise NexusError(f"Unrecognized input: {input[:100]} ...") from None
         file_contents = file_contents.strip()
         if file_contents.startswith("#NEXUS"):

Bio/SeqIO/SffIO.py

@@ -438,7 +438,6 @@ def _sff_do_slow_index(handle):
                     "byte padding region contained data" % padding,
                     BiopythonParserWarning,
                 )
-        # print("%s %s %i" % (read, name, record_offset))
         yield name, record_offset
     if handle.tell() % 8 != 0:
         raise ValueError("After scanning reads, did not end on a multiple of 8")

Bio/SeqIO/_index.py

@@ -642,7 +642,6 @@ class FastqRandomAccess(SeqFileRandomAccess):
                 raise ValueError("Problem with quality section")
             yield id.decode(), start_offset, length
             start_offset = end_offset
-        # print("EOF")
 
     def get_raw(self, offset):
         """Return the raw record from the file as a bytes string."""

Bio/SeqUtils/IsoelectricPoint.py

@@ -159,3 +159,9 @@ class IsoelectricPoint:
             next_pH = (min_ + max_) / 2
             return self.pi(next_pH, min_, max_)
         return pH
+
+
+if __name__ == "__main__":
+    from Bio._utils import run_doctest
+
+    run_doctest()

Bio/Sequencing/Ace.py

@@ -39,7 +39,7 @@ sorted into the right place.
 
 see _RecordConsumer for details.
 
-The second option is to  iterate over the contigs of an ace file one by one
+The second option is to iterate over the contigs of an ace file one by one
 in the usual way::
 
     from Bio.Sequencing import Ace

Bio/Sequencing/Phd.py

@@ -197,3 +197,9 @@ def _read(handle):
         record.seq_trimmed = record.seq[first:last]
 
     return record
+
+
+if __name__ == "__main__":
+    from Bio._utils import run_doctest
+
+    run_doctest()

Bio/SwissProt/KeyWList.py

@@ -6,7 +6,6 @@
 """Code to parse the keywlist.txt file from SwissProt/UniProt.
 
 See:
- - https://www.uniprot.org/docs/keywlist
  - https://www.uniprot.org/docs/keywlist.txt
 
 Classes:
@@ -85,7 +84,7 @@ def parse(handle):
             elif key in ("DE", "SY", "GO", "HI", "WW"):
                 record[key].append(value)
             else:
-                print(f"Ignoring: {line.strip()}")
+                raise ValueError(f"Cannot parse line '{line.strip()}'")
     # Read the footer and throw it away
     for line in handle:
         pass

Bio/motifs/jaspar/db.py

@@ -737,8 +737,6 @@ class JASPAR5:
         if where_clauses:
             sql = "".join([sql, " where ", " and ".join(where_clauses)])
 
-        # print("sql = %s" % sql)
-
         cur.execute(sql)
         rows = cur.fetchall()
 

Bio/motifs/mast.py

@@ -131,3 +131,9 @@ def __make_diagram(record, sequence_tree):
     # remove 0-length gaps
     motifs_with_gaps = [s for s in motifs_with_gaps if s != "0"]
     return "-".join(motifs_with_gaps)
+
+
+if __name__ == "__main__":
+    from Bio._utils import run_doctest
+
+    run_doctest()

Bio/motifs/meme.py

@@ -193,3 +193,9 @@ def __convert_strand(strand):
         return "-"
     if strand == "plus" or strand == "none":
         return "+"
+
+
+if __name__ == "__main__":
+    from Bio._utils import run_doctest
+
+    run_doctest()

Bio/motifs/minimal.py

@@ -191,3 +191,9 @@ def _read_motif_name(handle):
     words = line.split()
     name = " ".join(words[0:2])
     return name
+
+
+if __name__ == "__main__":
+    from Bio._utils import run_doctest
+
+    run_doctest()

Bio/phenotype/__init__.py

@@ -84,7 +84,7 @@ write in JSON format.
 """
 
 from Bio.File import as_handle
-from . import phen_micro
+from Bio.phenotype import phen_micro
 
 
 # Convention for format names is "mainname-format" in lower case.
@@ -226,3 +226,9 @@ def read(handle, format):
     if second is not None:
         raise ValueError("More than one record found in handle")
     return first
+
+
+if __name__ == "__main__":
+    from Bio._utils import run_doctest
+
+    run_doctest()

Tests/run_tests.py

@@ -64,6 +64,7 @@ EXCLUDE_DOCTEST_MODULES = ["Bio.Alphabet"]
 ONLINE_DOCTEST_MODULES = [
     "Bio.Entrez",
     "Bio.ExPASy",
+    "Bio.ExPASy.cellosaurus",
     "Bio.TogoWS",
 ]
 

Tests/test_SffIO.py

@@ -459,7 +459,6 @@ class TestSelf(unittest.TestCase):
 
             def fileiter(handle):
                 for record in SffIterator(handle):
-                    # print(record.id)
                     i = record.id
 
             self.assertRaises(ValueError, fileiter, handle)

Tests/test_pairwise_aligner.py

@@ -21,7 +21,6 @@ except ImportError:
 from Bio import Align, SeqIO
 from Bio.Seq import Seq, reverse_complement
 from Bio.SeqRecord import SeqRecord
-from Bio.SeqUtils import GC
 
 
 class TestAlignerProperties(unittest.TestCase):