Fixed sandbox files to use 'quality' instead of 'accuracy', fixes iss…

…ue 787

sandbox/collect-reads.py

@@ -26,8 +26,8 @@
 
 
 def output_single(read):
-    if hasattr(read, 'accuracy'):
-        return "@%s\n%s\n+\n%s\n" % (read.name, read.sequence, read.accuracy)
+    if hasattr(read, 'quality'):
+        return "@%s\n%s\n+\n%s\n" % (read.name, read.sequence, read.quality)
     else:
         return ">%s\n%s\n" % (read.name, read.sequence)
 

sandbox/correct-errors.py

@@ -38,17 +38,17 @@ def output_single(read, new_sequence):
     name = read.name
     sequence = new_sequence
 
-    accuracy = None
-    if hasattr(read, 'accuracy'):
-        accuracy = read.accuracy[:len(sequence)]
+    quality = None
+    if hasattr(read, 'quality'):
+        quality = read.quality[:len(sequence)]
 
         # in cases where sequence _lengthened_, need to truncate it to
         # match the quality score length.
-        sequence = sequence[:len(accuracy)]
+        sequence = sequence[:len(quality)]
 
-    if accuracy:
-        assert len(sequence) == len(accuracy), (sequence, accuracy)
-        return "@%s\n%s\n+\n%s\n" % (name, sequence, accuracy)
+    if quality:
+        assert len(sequence) == len(quality), (sequence, quality)
+        return "@%s\n%s\n+\n%s\n" % (name, sequence, quality)
     else:
         return ">%s\n%s\n" % (name, sequence)
 

sandbox/normalize-by-median-pct.py

@@ -139,10 +139,10 @@ def main():
             # Emit records if any passed
             if passed_length and passed_filter:
                 for record in batch:
-                    if hasattr(record, 'accuracy'):
+                    if hasattr(record, 'quality'):
                         outfp.write('@%s\n%s\n+\n%s\n' % (record.name,
                                                           record.sequence,
-                                                          record.accuracy))
+                                                          record.quality))
                     else:
                         outfp.write('>%s\n%s\n' %
                                     (record.name, record.sequence))

sandbox/slice-reads-by-coverage.py

@@ -6,8 +6,8 @@
 
 
 def output_single(read):
-    if hasattr(read, 'accuracy'):
-        return "@%s\n%s\n+\n%s\n" % (read.name, read.sequence, read.accuracy)
+    if hasattr(read, 'quality'):
+        return "@%s\n%s\n+\n%s\n" % (read.name, read.sequence, read.quality)
     else:
         return ">%s\n%s\n" % (read.name, read.sequence)
 

sandbox/sweep-files.py

@@ -69,8 +69,8 @@ def get_parser():
 
 
 def output_single(r):
-    if hasattr(r, 'accuracy'):
-        return "@%s\n%s\n+\n%s\n" % (r.name, r.sequence, r.accuracy)
+    if hasattr(r, 'quality'):
+        return "@%s\n%s\n+\n%s\n" % (r.name, r.sequence, r.quality)
     else:
         return ">%s\n%s\n" % (r.name, r.sequence)
 

sandbox/sweep-reads3.py

@@ -23,8 +23,8 @@
 
 
 def output_single(r):
-    if hasattr(r, 'accuracy'):
-        return "@%s\n%s\n+\n%s\n" % (r.name, r.sequence, r.accuracy)
+    if hasattr(r, 'quality'):
+        return "@%s\n%s\n+\n%s\n" % (r.name, r.sequence, r.quality)
     else:
         return ">%s\n%s\n" % (r.name, r.sequence)
 

sandbox/to-casava-1.8-fastq.py

@@ -47,10 +47,10 @@ def main():
             new_name = resub_read_2(new_name)
 
             output_file.write(
-                "@{name}\n{sequence}\n+\n{accuracy}\n".format(
+                "@{name}\n{sequence}\n+\n{quality}\n".format(
                     name=new_name,
                     sequence=read.sequence,
-                    accuracy=read.accuracy,
+                    quality=read.quality,
                 )
             )