# HG changeset patch
# User peterjc
# Date 1494941810 14400
# Node ID b9dc7c967ee6beb0b2a2e867e62aea3d65494a01
# Parent  530c8d6fedd890bdfd9d599f232397b6c54055dd
v0.0.16 Python 3 compatible print function

diff -r 530c8d6fedd8 -r b9dc7c967ee6 tools/seq_primer_clip/README.rst
--- a/tools/seq_primer_clip/README.rst	Wed May 10 13:09:52 2017 -0400
+++ b/tools/seq_primer_clip/README.rst	Tue May 16 09:36:50 2017 -0400
@@ -73,6 +73,7 @@
         - Explicit dependency on ``galaxy_sequence_utils``.
 v0.0.15 - Use ``<command detect_errors="aggressive">`` (internal change only).
         - Single quote command line arguments (internal change only)
+v0.0.16 - Python 3 compatible print function.
 ======= ======================================================================
 
 
diff -r 530c8d6fedd8 -r b9dc7c967ee6 tools/seq_primer_clip/seq_primer_clip.py
--- a/tools/seq_primer_clip/seq_primer_clip.py	Wed May 10 13:09:52 2017 -0400
+++ b/tools/seq_primer_clip/seq_primer_clip.py	Tue May 16 09:36:50 2017 -0400
@@ -33,13 +33,13 @@
 import re
 import sys
 
+if "-v" in sys.argv or "--version" in sys.argv:
+    print("v0.0.16")
+    sys.exit(0)
+
 from galaxy_utils.sequence.fasta import fastaReader, fastaWriter
 from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
 
-if "-v" in sys.argv or "--version" in sys.argv:
-    print "v0.0.12"
-    sys.exit(0)
-
 try:
     from Bio.Seq import reverse_complement
     from Bio.SeqIO.SffIO import SffIterator, SffWriter
@@ -130,10 +130,12 @@
 
 
 def make_reg_ex(seq):
+    """Make regular expression for ambiguous DNA."""
     return "".join(ambiguous_dna_re[letter] for letter in seq)
 
 
 def make_reg_ex_mm(seq, mm):
+    """Make regular expression for mis-matches."""
     if mm > 2:
         raise NotImplementedError("At most 2 mismatches allowed!")
     seq = seq.upper()
@@ -166,7 +168,10 @@
 
 
 def load_primers_as_re(primer_fasta, mm, rc=False):
-    # Read primer file and record all specified sequences
+    """Load primers as regular expressions.
+
+    Read primer file and record all specified sequences.
+    """
     primers = set()
     in_handle = open(primer_fasta, "rU")
     reader = fastaReader(in_handle)
@@ -189,7 +194,7 @@
 
 # Read primer file and record all specified sequences
 count, primer = load_primers_as_re(primer_fasta, mm, rc)
-print "%i primer sequences" % count
+print("%i primer sequences" % count)
 
 short_neg = 0
 short_clipped = 0
@@ -350,8 +355,8 @@
 in_handle.close()
 out_handle.close()
 
-print "Kept %i clipped reads," % clipped
-print "discarded %i short." % short_clipped
+print("Kept %i clipped reads," % clipped)
+print("discarded %i short." % short_clipped)
 if keep_negatives:
-    print "Kept %i non-matching reads," % negs
-    print "discarded %i short." % short_neg
+    print("Kept %i non-matching reads," % negs)
+    print("discarded %i short." % short_neg)
diff -r 530c8d6fedd8 -r b9dc7c967ee6 tools/seq_primer_clip/seq_primer_clip.xml
--- a/tools/seq_primer_clip/seq_primer_clip.xml	Wed May 10 13:09:52 2017 -0400
+++ b/tools/seq_primer_clip/seq_primer_clip.xml	Tue May 16 09:36:50 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.15">
+<tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.16">
     <description>Trim off 5' or 3' primers</description>
     <requirements>
         <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement>