diff fastq_groomer.py @ 0:06c42572d7c0 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastq_groomer.py	Thu Jan 23 12:31:44 2014 -0500
@@ -0,0 +1,42 @@
+#Dan Blankenberg
+import sys
+from galaxy_utils.sequence.fastq import fastqReader, fastqVerboseErrorReader, fastqAggregator, fastqWriter
+
+def main():
+    input_filename = sys.argv[1]
+    input_type = sys.argv[2]
+    output_filename = sys.argv[3]
+    output_type = sys.argv[4]
+    force_quality_encoding = sys.argv[5]
+    summarize_input = sys.argv[6] == 'summarize_input'
+    if force_quality_encoding == 'None':
+        force_quality_encoding = None
+    
+    aggregator = fastqAggregator()
+    out = fastqWriter( open( output_filename, 'wb' ), format = output_type, force_quality_encoding = force_quality_encoding )
+    read_count = None
+    if summarize_input:
+        reader = fastqVerboseErrorReader
+    else:
+        reader = fastqReader
+    for read_count, fastq_read in enumerate( reader( open( input_filename ), format = input_type, apply_galaxy_conventions = True ) ):
+        if summarize_input:
+            aggregator.consume_read( fastq_read )
+        out.write( fastq_read )
+    out.close()
+    
+    if read_count is not None:
+        print "Groomed %i %s reads into %s reads." % ( read_count + 1, input_type, output_type )
+        if input_type != output_type and 'solexa' in [ input_type, output_type ]:
+            print "Converted between Solexa and PHRED scores."
+        if summarize_input:
+            print "Based upon quality and sequence, the input data is valid for: %s" % ( ", ".join( aggregator.get_valid_formats() )  or "None" )
+            ascii_range = aggregator.get_ascii_range()
+            decimal_range =  aggregator.get_decimal_range()
+            print "Input ASCII range: %s(%i) - %s(%i)" % ( repr( ascii_range[0] ), ord( ascii_range[0] ), repr( ascii_range[1] ), ord( ascii_range[1] ) ) #print using repr, since \x00 (null) causes info truncation in galaxy when printed
+            print "Input decimal range: %i - %i" % ( decimal_range[0], decimal_range[1] )        
+    else:
+        print "No valid FASTQ reads were provided."
+
+
+if __name__ == "__main__": main()