diff tools/fastq/fastq_to_tabular.py @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/fastq/fastq_to_tabular.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,38 @@
+#Dan Blankenberg
+import sys
+from galaxy_utils.sequence.fastq import fastqReader
+
+def stop_err( msg ):
+    sys.stderr.write( msg )
+    sys.exit()
+
+def main():
+    if len(sys.argv) != 5:
+        stop_err("Wrong number of arguments. Expect: fasta tabular desrc_split [type]")
+    input_filename = sys.argv[1]
+    output_filename = sys.argv[2]
+    descr_split = int( sys.argv[3] ) - 1
+    if descr_split < 0:
+        stop_err("Bad description split value (should be 1 or more)")
+    input_type = sys.argv[4] or 'sanger' #input type should ordinarily be unnecessary
+    
+    num_reads = None
+    fastq_read = None
+    out = open( output_filename, 'wb' )
+    if descr_split == 0:
+        #Don't divide the description into multiple columns
+        for num_reads, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ):
+            out.write( "%s\t%s\t%s\n" % ( fastq_read.identifier[1:].replace( '\t', ' ' ), fastq_read.sequence.replace( '\t', ' ' ), fastq_read.quality.replace( '\t', ' ' ) ) )
+    else:
+        for num_reads, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ):
+            words = fastq_read.identifier[1:].replace( '\t', ' ' ).split(None, descr_split)
+            #pad with empty columns if required
+            words += [""]*(descr_split-len(words))
+            out.write( "%s\t%s\t%s\n" % ("\t".join(words), fastq_read.sequence.replace( '\t', ' ' ), fastq_read.quality.replace( '\t', ' ' ) ) )
+    out.close()
+    if num_reads is None:
+        print "No valid FASTQ reads could be processed."
+    else:
+        print "%i FASTQ reads were converted to Tabular." % ( num_reads + 1 )
+    
+if __name__ == "__main__": main()