diff tools/seq_primer_clip/seq_primer_clip.py @ 5:530c8d6fedd8 draft

v0.0.15 - internal changes

--- a/tools/seq_primer_clip/seq_primer_clip.py	Thu Feb 02 11:52:37 2017 -0500
+++ b/tools/seq_primer_clip/seq_primer_clip.py	Wed May 10 13:09:52 2017 -0400
@@ -29,8 +29,10 @@
 NOTE: Currently it uses Python's regular expression engine for finding the
 primers, which for my needs is fast enough.
 """
+
+import re
 import sys
-import re
+
 from galaxy_utils.sequence.fasta import fastaReader, fastaWriter
 from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
 
@@ -147,8 +149,8 @@
             # We'll use a set to remove any duplicate patterns
             # if letter not in "NX":
             pattern = seq[:i] + "N" + seq[i + 1:]
-            assert len(pattern) == len(seq), "Len %s is %i, len %s is %i" \
-                   % (pattern, len(pattern), seq, len(seq))
+            assert len(pattern) == len(seq), ("Len %s is %i, len %s is %i"
+                                              % (pattern, len(pattern), seq, len(seq)))
             yield make_reg_ex(pattern)
     if mm >= 2:
         for i, letter in enumerate(seq):
@@ -158,8 +160,8 @@
                 # We'll use a set to remove any duplicate patterns
                 # if letter not in "NX":
                 pattern = seq[:i] + "N" + seq[i + 1:i + 1 + k] + "N" + seq[i + k + 2:]
-                assert len(pattern) == len(seq), "Len %s is %i, len %s is %i" \
-                       % (pattern, len(pattern), seq, len(seq))
+                assert len(pattern) == len(seq), ("Len %s is %i, len %s is %i"
+                                                  % (pattern, len(pattern), seq, len(seq)))
                 yield make_reg_ex(pattern)