diff RM_custom_search.py @ 14:62fefa284036 draft

Uploaded

--- a/RM_custom_search.py	Fri Feb 07 02:25:47 2020 -0500
+++ b/RM_custom_search.py	Fri Feb 07 06:06:47 2020 -0500
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/env python
 ''' RepeatMasker search against custom database
 input:
 - archive with sequencing data
@@ -57,7 +57,7 @@
 
 def summarizeRepeatMaskerOutput(htmlout = "summary.html"):
     cmd = os.path.dirname(os.path.abspath(__file__))+"/rmsk_summary_table_multiple.r"
-    args = [ cmd, "-f", "dir_CL*/reads.fas", "-r", "dir_CL*/reads.fas.out", "-o", "RM-custom_output_table"  ]
+    args = [ cmd, "dir_CL*/reads.fas", "dir_CL*/reads.fas.out", "RM-custom_output_table"  ]
     status=subprocess.call(args)
     cmd = cmd = os.path.dirname(os.path.abspath(__file__))+"/RM_html_report.R"
     args = [cmd, htmlout]