--- a/tools/blastxml_to_top_descr/blastxml_to_top_descr.py	Wed Jul 30 05:36:52 2014 -0400
+++ b/tools/blastxml_to_top_descr/blastxml_to_top_descr.py	Sun Sep 17 13:01:56 2023 +0000
@@ -6,25 +6,26 @@
 
 Assumes the hits are pre-sorted, so "best" 3 hits gives first 3 hits.
 """
+from __future__ import print_function
+
 import os
+import re
 import sys
-import re
 from optparse import OptionParser
 
 if "-v" in sys.argv or "--version" in sys.argv:
-    print "v0.1.0"
+    print("v0.1.2")
     sys.exit(0)
 
-if sys.version_info[:2] >= ( 2, 5 ):
+if sys.version_info[:2] >= (2, 5):
     import xml.etree.cElementTree as ElementTree
 else:
-    from galaxy import eggs
-    import pkg_resources; pkg_resources.require( "elementtree" )
+    from galaxy import eggs  # noqa - ignore flake8 F401
+    import pkg_resources
+
+    pkg_resources.require("elementtree")
     from elementtree import ElementTree
 
-def stop_err( msg ):
-    sys.stderr.write("%s\n" % msg)
-    sys.exit(1)
 
 usage = """Use as follows:
 
@@ -39,23 +40,54 @@
 """
 
 parser = OptionParser(usage=usage)
-parser.add_option("-t", "--topN", dest="topN", default=3,
-                  help="Number of descriptions to collect (in order from file)")
-parser.add_option("-o", "--output", dest="out_file", default=None,
-                  help="Output filename for tabular file",
-                  metavar="FILE")
-parser.add_option("-f", "--format", dest="format", default="blastxml",
-                  help="Input format (blastxml or tabular)")
-parser.add_option("-q", "--qseqid", dest="qseqid", default="1",
-                  help="Column for query 'qseqid' (for tabular input; default 1)")
-parser.add_option("-s", "--sseqid", dest="sseqid", default="2",
-                  help="Column for subject 'sseqid' (for tabular input; default 2)")
-parser.add_option("-d", "--salltitles", dest="salltitles", default="25",
-                  help="Column for descriptions 'salltitles' (for tabular input; default 25)")
+parser.add_option(
+    "-t",
+    "--topN",
+    dest="topN",
+    default=3,
+    help="Number of descriptions to collect (in order from file)",
+)
+parser.add_option(
+    "-o",
+    "--output",
+    dest="out_file",
+    default=None,
+    help="Output filename for tabular file",
+    metavar="FILE",
+)
+parser.add_option(
+    "-f",
+    "--format",
+    dest="format",
+    default="blastxml",
+    help="Input format (blastxml or tabular)",
+)
+parser.add_option(
+    "-q",
+    "--qseqid",
+    dest="qseqid",
+    default="1",
+    help="Column for query 'qseqid' (for tabular input; default 1)",
+)
+parser.add_option(
+    "-s",
+    "--sseqid",
+    dest="sseqid",
+    default="2",
+    help="Column for subject 'sseqid' (for tabular input; default 2)",
+)
+parser.add_option(
+    "-d",
+    "--salltitles",
+    dest="salltitles",
+    default="25",
+    help="Column for descriptions 'salltitles' (for tabular input; default 25)",
+)
 (options, args) = parser.parse_args()
 
 if len(sys.argv) == 4 and len(args) == 3 and not options.out_file:
-    stop_err("""The API has changed, replace this:
+    sys.exit(
+        """The API has changed, replace this:
 
 $ python blastxml_to_top_descr.py input.xml output.tab 3
 
@@ -64,12 +96,13 @@
 $ python blastxml_to_top_descr.py -o output.tab -t 3 input.xml
 
 Sorry.
-""")
+"""
+    )
 
 if not args:
-    stop_err("Input filename missing, try -h")
+    sys.exit("Input filename missing, try -h")
 if len(args) > 1:
-    stop_err("Expects a single argument, one input filename")
+    sys.exit("Expects a single argument, one input filename")
 in_file = args[0]
 out_file = options.out_file
 topN = options.topN
@@ -77,12 +110,12 @@
 try:
     topN = int(topN)
 except ValueError:
-    stop_err("Number of hits  argument should be an integer (at least 1)")
+    sys.exit("Number of hits  argument should be an integer (at least 1)")
 if topN < 1:
-    stop_err("Number of hits  argument should be an integer (at least 1)")
+    sys.exit("Number of hits  argument should be an integer (at least 1)")
 
 if not os.path.isfile(in_file):
-    stop_err("Missing input file: %r" % in_file)
+    sys.exit("Missing input file: %r" % in_file)
 
 
 def get_column(value):
@@ -92,11 +125,12 @@
         value = value[1:]
     try:
         col = int(value)
-    except:
-        stop_err("Expected an integer column number, not %r" % value)
+    except ValueError:
+        sys.exit("Expected an integer column number, not %r" % value)
     if col < 1:
-        stop_err("Expect column numbers to be at least one, not %r" % value)
-    return col - 1 # Python counting!
+        sys.exit("Expect column numbers to be at least one, not %r" % value)
+    return col - 1  # Python counting!
+
 
 def tabular_hits(in_file, qseqid, sseqid, salltitles):
     """Parse key data from tabular BLAST output.
@@ -105,8 +139,8 @@
     """
     current_query = None
     current_hits = []
-    with open(in_file) as input:
-        for line in input:
+    with open(in_file) as input_handle:
+        for line in input_handle:
             parts = line.rstrip("\n").split("\t")
             query = parts[qseqid]
             descr = "%s %s" % (parts[sseqid], parts[salltitles])
@@ -126,6 +160,7 @@
         # Final query
         yield current_query, current_hits
 
+
 def blastxml_hits(in_file):
     """Parse key data from BLAST XML output.
 
@@ -133,32 +168,35 @@
     """
     try:
         context = ElementTree.iterparse(in_file, events=("start", "end"))
-    except:
+    except Exception:
         with open(in_file) as handle:
             header = handle.read(100)
-        stop_err("Invalid data format in XML file %r which starts: %r" % (in_file, header))
+        sys.exit(
+            "Invalid data format in XML file %r which starts: %r" % (in_file, header)
+        )
     # turn it into an iterator
     context = iter(context)
     # get the root element
     try:
-        event, root = context.next()
-    except:
+        event, root = next(context)
+    except Exception:
         with open(in_file) as handle:
             header = handle.read(100)
-        stop_err("Unable to get root element from XML file %r which starts: %r" % (in_file, header))
+        sys.exit(
+            "Unable to get root element from XML file %r which starts: %r"
+            % (in_file, header)
+        )
 
-    re_default_query_id = re.compile("^Query_\d+$")
-    assert re_default_query_id.match("Query_101")
-    assert not re_default_query_id.match("Query_101a")
-    assert not re_default_query_id.match("MyQuery_101")
-    re_default_subject_id = re.compile("^Subject_\d+$")
-    assert re_default_subject_id.match("Subject_1")
-    assert not re_default_subject_id.match("Subject_")
-    assert not re_default_subject_id.match("Subject_12a")
-    assert not re_default_subject_id.match("TheSubject_1")
+    re_default_query_id = re.compile(r"^Query_\d+$")
+    assert re_default_query_id.match(r"Query_101")
+    assert not re_default_query_id.match(r"Query_101a")
+    assert not re_default_query_id.match(r"MyQuery_101")
+    re_default_subject_id = re.compile(r"^Subject_\d+$")
+    assert re_default_subject_id.match(r"Subject_1")
+    assert not re_default_subject_id.match(r"Subject_")
+    assert not re_default_subject_id.match(r"Subject_12a")
+    assert not re_default_subject_id.match(r"TheSubject_1")
 
-    count = 0
-    pos_count = 0
     current_query = None
     hit_descrs = []
     for event, elem in context:
@@ -166,7 +204,8 @@
         if event == "end" and elem.tag == "Iteration":
             # Expecting either this, from BLAST 2.2.25+ using FASTA vs FASTA
             # <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>
-            # <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
+            # <Iteration_query-def>Endoplasmic reticulum resident protein 44
+            # OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
             # <Iteration_query-len>406</Iteration_query-len>
             # <Iteration_hits></Iteration_hits>
             #
@@ -177,10 +216,12 @@
             # <Iteration_hits>...
             qseqid = elem.findtext("Iteration_query-ID")
             if qseqid is None:
-                stop_err("Missing <Iteration_query-ID> (could be really old BLAST XML data?)")
+                sys.exit(
+                    "Missing <Iteration_query-ID> (could be really old BLAST XML data?)"
+                )
             if re_default_query_id.match(qseqid):
-                #Place holder ID, take the first word of the query definition
-                qseqid = elem.findtext("Iteration_query-def").split(None,1)[0]
+                # Place holder ID, take the first word of the query definition
+                qseqid = elem.findtext("Iteration_query-def").split(None, 1)[0]
             if current_query is None:
                 # First hit
                 current_query = qseqid
@@ -203,17 +244,19 @@
                 # <Hit_accession>P56514</Hit_accession>
                 # or,
                 # <Hit_id>Subject_1</Hit_id>
-                # <Hit_def>gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus]</Hit_def>
+                # <Hit_def>gi|57163783|ref|NP_001009242.1|
+                # rhodopsin [Felis catus]</Hit_def>
                 # <Hit_accession>Subject_1</Hit_accession>
                 #
-                #apparently depending on the parse_deflines switch
-                sseqid = hit.findtext("Hit_id").split(None,1)[0]
+                # apparently depending on the parse_deflines switch
+                sseqid = hit.findtext("Hit_id").split(None, 1)[0]
                 hit_def = sseqid + " " + hit.findtext("Hit_def")
-                if re_default_subject_id.match(sseqid) \
-                and sseqid == hit.findtext("Hit_accession"):
-                    #Place holder ID, take the first word of the subject definition
+                if re_default_subject_id.match(sseqid) and sseqid == hit.findtext(
+                    "Hit_accession"
+                ):
+                    # Place holder ID, take the first word of the subject definition
                     hit_def = hit.findtext("Hit_def")
-                    sseqid = hit_def.split(None,1)[0]
+                    sseqid = hit_def.split(None, 1)[0]
                 assert hit_def not in hit_descrs
                 hit_descrs.append(hit_def)
             # prevents ElementTree from growing large datastructure
@@ -223,6 +266,7 @@
         # Final query
         yield current_query, hit_descrs
 
+
 if options.format == "blastxml":
     hits = blastxml_hits(in_file)
 elif options.format == "tabular":
@@ -231,21 +275,23 @@
     salltitles = get_column(options.salltitles)
     hits = tabular_hits(in_file, qseqid, sseqid, salltitles)
 else:
-    stop_err("Unsupported format: %r" % options.format)
+    sys.exit("Unsupported format: %r" % options.format)
 
 
 def best_hits(descriptions, topN):
+    """Truncate given descriptions list to at most N entries."""
     if len(descriptions) < topN:
-        return descriptions +  [""] * (topN - len(descriptions))
+        return descriptions + [""] * (topN - len(descriptions))
     else:
         return descriptions[:topN]
 
+
 count = 0
 if out_file is None:
     outfile = sys.stdout
 else:
-    outfile = open(out_file, 'w')
-outfile.write("#Query\t%s\n" % "\t".join("BLAST hit %i" % (i+1) for i in range(topN)))
+    outfile = open(out_file, "w")
+outfile.write("#Query\t%s\n" % "\t".join("BLAST hit %i" % (i + 1) for i in range(topN)))
 for query, descrs in hits:
     count += 1
     outfile.write("%s\t%s\n" % (query, "\t".join(best_hits(descrs, topN))))