diff bowtie_rRNA_removal_wrapper/bowtie_rRNA_tRNA_removal_wrapper.py @ 21:b49ad9f12dfa draft

Uploaded

--- a/bowtie_rRNA_removal_wrapper/bowtie_rRNA_tRNA_removal_wrapper.py	Wed Apr 13 09:00:19 2022 +0000
+++ b/bowtie_rRNA_removal_wrapper/bowtie_rRNA_tRNA_removal_wrapper.py	Wed May 11 13:37:35 2022 +0000
@@ -411,10 +411,19 @@
         # have to nest try-except in try-finally to handle 2.4
         try:
             # prepare actual mapping commands
-            if options.paired == 'paired':
-                cmd2 = 'bowtie %s %s -1 %s -2 %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.input2, options.output )
+            if options.output != 'XXXX':
+                print('incorrect option')
+                if options.paired == 'paired':
+                    cmd2 = 'bowtie %s %s -1 %s -2 %s > %s | samtools view -b -S > %s' % ( aligning_cmds, ref_file_name, options.input1, options.input2, options.output, options.output )
+                else:
+                    cmd2 = 'bowtie %s %s %s > %s | samtools view -b -S > %s' % ( aligning_cmds, ref_file_name, options.input1, options.output, options.output )
             else:
-                cmd2 = 'bowtie %s %s %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.output )
+                if options.paired == 'paired':
+                    cmd2 = 'bowtie %s %s -1 %s -2 %s' % ( aligning_cmds, ref_file_name, options.input1, options.input2 )
+                else:
+                    print('correct option')
+                    cmd2 = 'bowtie %s %s %s' % ( aligning_cmds, ref_file_name, options.input1 )
+                    print(cmd2)
             # align
             tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
             with open(tmp, 'w') as tmp_stderr:
@@ -456,7 +465,7 @@
                 except Exception as e:
                     sys.stdout.write( 'Error producing the unmapped output file.\n' )
             # check that there are results in the output file
-            if os.path.getsize( options.output ) == 0:
+            if options.output != "XXXX" and os.path.getsize( options.output ) == 0:
                 raise Exception('The output file is empty, there may be an error with your input file or settings.')
         except Exception as e:
             stop_err( 'Error aligning sequence. ' + str( e ) )