Mercurial > repos > tyty > structurefold

diff Iterative_mapping/iterative_map.py @ 112:87ec0ecdc2af draft

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Uploaded
author tyty
date Sun, 12 Apr 2015 14:28:30 -0400
parents b6bdd41440f3
children
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line diff
--- a/Iterative_mapping/iterative_map.py	Sun Mar 29 01:21:50 2015 -0400
+++ b/Iterative_mapping/iterative_map.py	Sun Apr 12 14:28:30 2015 -0400
@@ -103,10 +103,7 @@
         break
     os.system("rm "+syspathrs+"count"+str(k+1)+".txt")
     k = k+1
-    if type_input == "fasta":
-        os.system("bowtie "+s+"-f "+syspathrs+"ref"+" "+syspathrs+"seq"+str(k)+".fa --quiet -S > "+syspathrs+"map"+str(k)+".sam")
-    if type_input == "fastq":
-        os.system("bowtie "+s+"-q "+syspathrs+"ref"+" "+syspathrs+"seq"+str(k)+".fa --quiet -S > "+syspathrs+"map"+str(k)+".sam")
+    os.system("bowtie "+s+"-f "+syspathrs+"ref"+" "+syspathrs+"seq"+str(k)+".fa --quiet -S > "+syspathrs+"map"+str(k)+".sam")
 
 
 ss = ""