From bf9666bf215767f1cc30fe5d2d2ce154f12d869b Mon Sep 17 00:00:00 2001
From: Anton Nekrutenko <anton@bx.psu.edu>
Date: Thu, 20 Aug 2009 17:33:39 -0400
Subject: [PATCH] Fixed a stupid and truly horrible paired end splitter bug

---
 static/welcome.html                     |  2 +-
 tools/metag_tools/split_paired_reads.py | 14 +++++++++++---
 tools/solid_tools/maq_cs_wrapper.py     |  8 ++++----
 3 files changed, 16 insertions(+), 8 deletions(-)

diff --git a/static/welcome.html b/static/welcome.html
index b64180964ca..4bbb02cae90 100644
--- a/static/welcome.html
+++ b/static/welcome.html
@@ -71,7 +71,7 @@
         <table border="0" cellpadding="0" cellspacing="0" width="100%">
             <tr>
                 <td>
-                    <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie1_TabSeq/flow.html',width:640,height:500,scroll:'no'})">
+                    <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie1_TabSeq/quickie1_TabSeq.flv',width:640,height:500,scroll:'no'})">
 	                   <div class="quickie">
                         <img src="images/qk/quickie1_small.png" border="0">
 	                   </div>
diff --git a/tools/metag_tools/split_paired_reads.py b/tools/metag_tools/split_paired_reads.py
index f2e4039e5a6..f2b01bc7b35 100644
--- a/tools/metag_tools/split_paired_reads.py
+++ b/tools/metag_tools/split_paired_reads.py
@@ -1,7 +1,7 @@
 #! /usr/bin/python
 
 """
-Split Solexa paired end reads
+Split fixed length paired end reads
 """
 
 import os, sys
@@ -12,9 +12,13 @@ if __name__ == '__main__':
     outfile_end1 = open(sys.argv[2], 'w')
     outfile_end2 = open(sys.argv[3], 'w')
     
-    for i, line in enumerate(file(infile)):
+    i = 0
+    
+    for line in file( infile ):
         line = line.rstrip()
-        if not line or line.startswith('#'): continue
+        
+        if not line:
+            continue 
         
         end1 = ''
         end2 = ''
@@ -42,5 +46,9 @@ if __name__ == '__main__':
         outfile_end1.write('%s\n' %(end1))
         outfile_end2.write('%s\n' %(end2))
         
+        i += 1
+        
+    if  i % 4 != 0  :
+        sys.stderr.write("WARNING: Number of lines in the input file was not divisible by 4.\nCheck consistency of the input fastq file.\n")
     outfile_end1.close()
     outfile_end2.close()    
\ No newline at end of file
diff --git a/tools/solid_tools/maq_cs_wrapper.py b/tools/solid_tools/maq_cs_wrapper.py
index 82f29270975..e0c305dd9eb 100644
--- a/tools/solid_tools/maq_cs_wrapper.py
+++ b/tools/solid_tools/maq_cs_wrapper.py
@@ -48,9 +48,9 @@ def __main__():
         cmd1 = "solid2fastq_modified.pl 'yes' %s %s %s %s %s %s %s 2>&1" %(tmpf.name,tmpr.name,tmps.name,f3_read_fname,f3_qual_fname,r3_read_fname,r3_qual_fname)
         try:
             os.system(cmd1)
-            os.system('zcat -f %s >> %s' %(tmpf.name,tmpffastq.name))
-            os.system('zcat -f %s >> %s' %(tmpr.name,tmprfastq.name))
-            os.system('zcat -f %s >> %s' %(tmps.name,tmpsfastq.name))
+            os.system('gunzip -c %s >> %s' %(tmpf.name,tmpffastq.name))
+            os.system('gunzip -c %s >> %s' %(tmpr.name,tmprfastq.name))
+            os.system('gunzip -c %s >> %s' %(tmps.name,tmpsfastq.name))
 
         except Exception, eq:
             stop_err("Error converting data to fastq format." + str(eq))
@@ -135,7 +135,7 @@ def __main__():
         cmd1 = "solid2fastq_modified.pl 'no' %s %s %s %s %s %s %s 2>&1" %(tmpf.name,None,None,f3_read_fname,f3_qual_fname,None,None)
         try:
             os.system(cmd1)
-            os.system('zcat -f %s >> %s' %(tmpf.name,tmpfastq.name))
+            os.system('gunzip -c %s >> %s' %(tmpf.name,tmpfastq.name))
             tmpf.close()
         except:
             stop_err("Error converting data to fastq format.")