diff fastq_to_fasta.py @ 0:3571553aeb20 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastq_to_fasta.py	Mon Jan 27 09:27:22 2014 -0500
@@ -0,0 +1,22 @@
+#Dan Blankenberg
+import sys
+from galaxy_utils.sequence.fastq import fastqReader
+from galaxy_utils.sequence.fasta import fastaWriter
+
+def main():
+    input_filename = sys.argv[1]
+    output_filename = sys.argv[2]
+    input_type = sys.argv[3] or 'sanger' #input type should ordinarily be unnecessary
+    
+    num_reads = None
+    fastq_read = None
+    out = fastaWriter( open( output_filename, 'wb' ) )
+    for num_reads, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ):
+        out.write( fastq_read )
+    out.close()
+    if num_reads is None:
+        print "No valid FASTQ reads could be processed."
+    else:
+        print "%i FASTQ reads were converted to FASTA." % ( num_reads + 1 )
+    
+if __name__ == "__main__": main()