diff fastq_trimmer.py @ 0:feb5479a48ff draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastq_trimmer.py	Thu Jan 23 12:31:36 2014 -0500
@@ -0,0 +1,41 @@
+#Dan Blankenberg
+import sys
+from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
+
+def main():
+    input_filename = sys.argv[1]
+    output_filename = sys.argv[2]
+    left_offset = sys.argv[3]
+    right_offset = sys.argv[4]
+    percent_offsets = sys.argv[5] == 'offsets_percent'
+    input_type = sys.argv[6] or 'sanger'
+    keep_zero_length = sys.argv[7] == 'keep_zero_length'
+    
+    out = fastqWriter( open( output_filename, 'wb' ), format = input_type )
+    num_reads_excluded = 0
+    num_reads = None
+    for num_reads, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ):
+        if percent_offsets:
+            left_column_offset = int( round( float( left_offset ) / 100.0 * float( len( fastq_read ) ) ) )
+            right_column_offset = int( round( float( right_offset ) / 100.0 * float( len( fastq_read ) ) ) )
+        else:
+            left_column_offset = int( left_offset )
+            right_column_offset = int( right_offset )
+        if right_column_offset > 0:
+            right_column_offset = -right_column_offset
+        else:
+            right_column_offset = None
+        fastq_read = fastq_read.slice( left_column_offset, right_column_offset )
+        if keep_zero_length or len( fastq_read ):
+            out.write( fastq_read )
+        else:
+            num_reads_excluded += 1
+    out.close()
+    if num_reads is None:
+        print "No valid fastq reads could be processed."
+    else:
+        print "%i fastq reads were processed." % ( num_reads + 1 )
+    if num_reads_excluded:
+        print "%i reads of zero length were excluded from the output." % num_reads_excluded
+
+if __name__ == "__main__": main()