diff tabular_to_fastq.py @ 3:643018aa1435 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit f2582539542b33240234e8ea6093e25d0aee9b6a

--- a/tabular_to_fastq.py	Fri Dec 18 19:31:46 2015 -0500
+++ b/tabular_to_fastq.py	Sat Sep 30 13:54:43 2017 -0400
@@ -1,29 +1,33 @@
-#Dan Blankenberg
+# Dan Blankenberg
+from __future__ import print_function
+
 import sys
 
+
 def main():
     input_filename = sys.argv[1]
     output_filename = sys.argv[2]
-    identifier_col = int( sys.argv[3] ) - 1
-    sequence_col = int( sys.argv[4] ) - 1
-    quality_col = int( sys.argv[5] ) - 1
-    
-    max_col = max( identifier_col, sequence_col, quality_col )
+    identifier_col = int(sys.argv[3]) - 1
+    sequence_col = int(sys.argv[4]) - 1
+    quality_col = int(sys.argv[5]) - 1
+
+    max_col = max(identifier_col, sequence_col, quality_col)
     num_reads = None
-    fastq_read = None
     skipped_lines = 0
-    out = open( output_filename, 'wb' )
-    for num_reads, line in enumerate( open( input_filename ) ):
-        fields = line.rstrip( '\n\r' ).split( '\t' )
-        if len( fields ) > max_col:
-            out.write( "@%s\n%s\n+\n%s\n" % ( fields[identifier_col], fields[sequence_col], fields[quality_col] ) )
+    out = open(output_filename, 'w')
+    for num_reads, line in enumerate(open(input_filename)):
+        fields = line.rstrip('\n\r').split('\t')
+        if len(fields) > max_col:
+            out.write("@%s\n%s\n+\n%s\n" % (fields[identifier_col], fields[sequence_col], fields[quality_col]))
         else:
             skipped_lines += 1
-    
+
     out.close()
     if num_reads is None:
-        print "Input was empty."
+        print("Input was empty.")
     else:
-        print "%i tabular lines were written as FASTQ reads. Be sure to use the FASTQ Groomer tool on this output before further analysis." % ( num_reads + 1 - skipped_lines )
-    
-if __name__ == "__main__": main()
+        print("%i tabular lines were written as FASTQ reads. Be sure to use the FASTQ Groomer tool on this output before further analysis." % (num_reads + 1 - skipped_lines))
+
+
+if __name__ == "__main__":
+    main()