Fixed bug in CloseMatch where end location was incorrectly computed; and updated partial_gene_match.py example.

3 files changed, 56 insertions, 90 deletions

diff --git a/CHANGES b/CHANGES
index 612de6c..68503c7 100644
--- a/CHANGES
+++ b/CHANGES
@@ -38,6 +38,9 @@ Version 2.5.0a1
   suppression. As part of resolution to a question posted by John
   Greene on StackOverflow.
 
+- Fixed bug in CloseMatch where end location was incorrectly
+  computed; and updated partial_gene_match.py example.
+
 - BigQueryViewParser.py added to examples directory, PR submitted
   by Michael Smedberg, nice work!
 
diff --git a/examples/partial_gene_match.py b/examples/partial_gene_match.py
index e19cf8b..8ca9c44 100644
--- a/examples/partial_gene_match.py
+++ b/examples/partial_gene_match.py
@@ -1,88 +1,51 @@
-# parital_gene_match.py

-#

-#  Example showing how to create a customized pyparsing Token, in this case,

-#  one that is very much like Literal, but which tolerates up to 'n' character

-#  mismatches

-from pyparsing import *

-

-import urllib.request, urllib.parse, urllib.error

-

-# read in a bunch of genomic data

-datafile = urllib.request.urlopen("http://toxodb.org/common/downloads/release-6.0/Tgondii/TgondiiApicoplastORFsNAs_ToxoDB-6.0.fasta")

-fastasrc = datafile.read()

-datafile.close()

-

-"""

-Sample header:

->NC_001799-6-2978-2778 | organism=Toxoplasma_gondii_RH | location=NC_001799:2778-2978(-) | length=201

-"""

-integer = Word(nums).setParseAction(lambda t:int(t[0]))

-genebit = Group(">" + Word(alphanums.upper()+"-_") + "|" +

-                Word(printables)("id") + SkipTo("length=", include=True) +

-                integer("genelen") + LineEnd() +

-                Combine(OneOrMore(Word("ACGTN")),adjacent=False)("gene"))

-

-# read gene data from .fasta file - takes just a few seconds

-genedata = OneOrMore(genebit).parseString(fastasrc)

-

-

-class CloseMatch(Token):

-    """A special subclass of Token that does *close* matches. For each

-       close match of the given string, a tuple is returned giving the

-       found close match, and a list of mismatch positions."""

-    def __init__(self, seq, maxMismatches=1):

-        super(CloseMatch,self).__init__()

-        self.name = seq

-        self.sequence = seq

-        self.maxMismatches = maxMismatches

-        self.errmsg = "Expected " + self.sequence

-        self.mayIndexError = False

-        self.mayReturnEmpty = False

-

-    def parseImpl( self, instring, loc, doActions=True ):

-        start = loc

-        instrlen = len(instring)

-        maxloc = start + len(self.sequence)

-

-        if maxloc <= instrlen:

-            seq = self.sequence

-            seqloc = 0

-            mismatches = []

-            throwException = False

-            done = False

-            while loc < maxloc and not done:

-                if instring[loc] != seq[seqloc]:

-                    mismatches.append(seqloc)

-                    if len(mismatches) > self.maxMismatches:

-                        throwException = True

-                        done = True

-                loc += 1

-                seqloc += 1

-        else:

-            throwException = True

-

-        if throwException:

-            exc = self.myException

-            exc.loc = loc

-            exc.pstr = instring

-            raise exc

-

-        return loc, (instring[start:loc],mismatches)

-

-# using the genedata extracted above, look for close matches of a gene sequence

-searchseq = CloseMatch("TTAAATCTAGAAGAT", 3)

-for g in genedata:

-    print("%s (%d)" % (g.id, g.genelen))

-    print("-"*24)

-    for t,startLoc,endLoc in searchseq.scanString(g.gene, overlap=True):

-        matched, mismatches = t[0]

-        print("MATCH:", searchseq.sequence)

-        print("FOUND:", matched)

-        if mismatches:

-            print("      ", ''.join(' ' if i not in mismatches else '*'

-                            for i,c in enumerate(searchseq.sequence)))

-        else:

-            print("<exact match>")

-        print("at location", startLoc)

-        print()

-    print()

+# parital_gene_match.py
+#
+#  Example showing how to use the CloseMatch class, to find strings in a gene with up to 'n' mismatches
+#
+import pyparsing as pp
+
+import urllib.request, urllib.parse, urllib.error
+from contextlib import closing
+
+# read in a bunch of genomic data
+data_url = "http://toxodb.org/common/downloads/release-6.0/Tgondii/TgondiiApicoplastORFsNAs_ToxoDB-6.0.fasta"
+with closing(urllib.request.urlopen(data_url)) as datafile:
+    fastasrc = datafile.read().decode()
+
+"""
+Sample header:
+>NC_001799-6-2978-2778 | organism=Toxoplasma_gondii_RH | location=NC_001799:2778-2978(-) | length=201
+"""
+integer = pp.Word(pp.nums).setParseAction(lambda t:int(t[0]))
+genebit = pp.Group(">" + pp.Word(pp.alphanums.upper() + "-_")("gene_id")
+                   + "|" + pp.Word(pp.printables)("organism")
+                   + "|" + pp.Word(pp.printables)("location")
+                   + "|" + "length=" + integer("gene_len")
+                   + pp.LineEnd()
+                   + pp.Word("ACGTN")[1, ...].addParseAction(''.join)("gene"))
+
+# read gene data from .fasta file - takes just a few seconds
+genedata = genebit[1, ...].parseString(fastasrc)
+
+# using the genedata extracted above, look for close matches of a gene sequence
+searchseq = pp.CloseMatch("TTAAATCTAGAAGAT", 3)
+
+for g in genedata:
+    show_header = True
+    for t, startLoc, endLoc in searchseq.scanString(g.gene, overlap=True):
+        if show_header:
+            print("%s/%s/%s (%d)" % (g.gene_id, g.organism, g.location, g.gene_len))
+            print("-" * 24)
+            show_header = False
+
+        matched = t[0]
+        mismatches = t['mismatches']
+        print("MATCH:", searchseq.match_string)
+        print("FOUND:", matched)
+        if mismatches:
+            print("      ", ''.join('*' if i in mismatches else ' '
+                                    for i, c in enumerate(searchseq.match_string)))
+        else:
+            print("<exact match>")
+        print("at location", startLoc)
+        print()
diff --git a/pyparsing.py b/pyparsing.py
index 92e2929..23b36dc 100644
--- a/pyparsing.py
+++ b/pyparsing.py
@@ -96,7 +96,7 @@ classes inherit from. Use the docstrings for examples of how to:
 """
 
 __version__ = "2.5.0a1"
-__versionTime__ = "06 Aug 2019 01:12 UTC"
+__versionTime__ = "06 Aug 2019 04:55 UTC"
 __author__ = "Paul McGuire <ptmcg@users.sourceforge.net>"
 
 import string
@@ -2843,7 +2843,7 @@ class CloseMatch(Token):
                     if len(mismatches) > maxMismatches:
                         break
             else:
-                loc = match_stringloc + 1
+                loc = start + match_stringloc + 1
                 results = ParseResults([instring[start:loc]])
                 results['original'] = match_string
                 results['mismatches'] = mismatches