diff tabular_to_fastq.py @ 0:9ae652b76979 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tabular_to_fastq.py	Thu Jan 23 12:31:40 2014 -0500
@@ -0,0 +1,29 @@
+#Dan Blankenberg
+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 )
+    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] ) )
+        else:
+            skipped_lines += 1
+    
+    out.close()
+    if num_reads is None:
+        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()