diff amplicon_analysis_pipeline.py @ 39:d19fca1c009c draft

planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit c3970ae16b02774148dbf950880f07255734a9a8-dirty

--- a/amplicon_analysis_pipeline.py	Wed Oct 17 05:01:57 2018 -0400
+++ b/amplicon_analysis_pipeline.py	Wed Oct 17 08:14:27 2018 -0400
@@ -97,15 +97,6 @@
     if filen is not None:
         fp.close()
 
-def find_executable(name):
-    # Locate executable on PATH
-    for p in os.environ['PATH'].split(os.pathsep):
-        exe = os.path.normpath(
-            os.path.abspath(os.path.join(p,name)))
-        if os.path.isfile(exe) and os.access(exe,os.X_OK):
-            return exe
-    return None
-
 if __name__ == "__main__":
     # Command line
     print "Amplicon analysis: starting"
@@ -149,11 +140,12 @@
 
     # Link to FASTQs and construct Final_name.txt file
     sample_names = []
+    print "-- making Final_name.txt"
     with open("Final_name.txt",'w') as final_name:
         fastqs = iter(args.fastq_pairs)
         for sample_name,fqr1,fqr2 in zip(fastqs,fastqs,fastqs):
             sample_name = clean_up_name(sample_name)
-            print "Cleaned up sample name: %s" % sample_name
+            print "   %s" % sample_name
             r1 = "%s_R1_.fastq" % sample_name
             r2 = "%s_R2_.fastq" % sample_name
             os.symlink(fqr1,r1)