diff fastq_filter.py @ 0:0017fa63af6c draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastq_filter.py	Thu Jan 23 12:31:42 2014 -0500
@@ -0,0 +1,36 @@
+#Dan Blankenberg
+import sys, os, shutil
+from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
+
+def main():
+    #Read command line arguments
+    input_filename = sys.argv[1]
+    script_filename = sys.argv[2]
+    output_filename = sys.argv[3]
+    additional_files_path = sys.argv[4]
+    input_type = sys.argv[5] or 'sanger'
+    
+    #Save script file for debuging/verification info later
+    os.mkdir( additional_files_path )
+    shutil.copy( script_filename, os.path.join( additional_files_path, 'debug.txt' ) )
+    
+    ## Dan, Others: Can we simply drop the "format=input_type" here since it is specified in reader.
+    ## This optimization would cut runtime roughly in half (for my test case anyway). -John
+    out = fastqWriter( open( output_filename, 'wb' ), format = input_type )
+    
+    i = None
+    reads_kept = 0
+    execfile(script_filename, globals())
+    for i, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ):
+        ret_val = fastq_read_pass_filter( fastq_read )  ## fastq_read_pass_filter defined in script_filename
+        if ret_val:
+            out.write( fastq_read )
+            reads_kept += 1
+    out.close()
+    if i is None:
+        print "Your file contains no valid fastq reads."
+    else:
+        print 'Kept %s of %s reads (%.2f%%).' % ( reads_kept, i + 1, float( reads_kept ) / float( i + 1 ) * 100.0 )
+
+if __name__ == "__main__":
+    main()