--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/next_gen_conversion/solid_to_fastq.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,68 @@
+#!/usr/bin/env python
+
+"""
+Converts SOLiD data to Sanger FASTQ format.
+
+usage: %prog [options]
+   -i, --input1=i: Forward reads file
+   -q, --input2=q: Forward qual file
+   -I, --input3=I: Reverse reads file
+   -Q, --input4=Q: Reverse qual file
+   -o, --output1=o: Forward output
+   -r, --output2=r: Reverse output
+
+usage: %prog forward_reads_file forwards_qual_file reverse_reads_file(or_None) reverse_qual_file(or_None) output_file ouptut_id output_dir
+"""
+
+import os, sys, tempfile
+from galaxy import eggs
+import pkg_resources; pkg_resources.require( "bx-python" )
+from bx.cookbook import doc_optparse
+
+def stop_err( msg ):
+    sys.stderr.write( "%s\n" % msg )
+    sys.exit()
+    
+def replaceNeg1(fin, fout):
+    line = fin.readline()
+    while line.strip():
+        fout.write(line.replace('-1', '1'))
+        line = fin.readline()
+    fout.seek(0)
+    return fout
+ 
+def __main__():
+    #Parse Command Line
+    options, args = doc_optparse.parse( __doc__ )
+    # common temp file setup
+    tmpf = tempfile.NamedTemporaryFile()    #forward reads
+    tmpqf = tempfile.NamedTemporaryFile()
+    tmpqf = replaceNeg1(file(options.input2,'r'), tmpqf)
+    # if paired-end data (have reverse input files)
+    if options.input3 != "None" and options.input4 != "None":
+        tmpr = tempfile.NamedTemporaryFile()    #reverse reads
+        # replace the -1 in the qualities file 
+        tmpqr = tempfile.NamedTemporaryFile()
+        tmpqr = replaceNeg1(file(options.input4,'r'), tmpqr)
+        cmd1 = "%s/bwa_solid2fastq_modified.pl 'yes' %s %s %s %s %s %s 2>&1" %(os.path.split(sys.argv[0])[0], tmpf.name, tmpr.name, options.input1, tmpqf.name, options.input3, tmpqr.name)
+        try:
+            os.system(cmd1)
+            os.system('gunzip -c %s >> %s' %(tmpf.name,options.output1))
+            os.system('gunzip -c %s >> %s' %(tmpr.name,options.output2))
+        except Exception, eq:
+            stop_err("Error converting data to fastq format.\n" + str(eq))
+        tmpr.close()
+        tmpqr.close()
+    # if single-end data
+    else:
+        cmd1 = "%s/bwa_solid2fastq_modified.pl 'no' %s %s %s %s %s %s 2>&1" % (os.path.split(sys.argv[0])[0], tmpf.name, None, options.input1, tmpqf.name, None, None)
+        try:
+            os.system(cmd1)
+            os.system('gunzip -c %s >> %s' % (tmpf.name, options.output1))
+        except Exception, eq:
+            stop_err("Error converting data to fastq format.\n" + str(eq))
+    tmpqf.close()
+    tmpf.close()
+    sys.stdout.write('converted SOLiD data')
+
+if __name__=="__main__": __main__()