Mercurial > repos > petr-novak > re_utils

diff RM_custom_search.py @ 32:628b235d76c7 draft

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planemo upload commit 39094a128ea3dd2c39f4997c6de739c33c07e5f3-dirty
author petr-novak
date Fri, 04 Aug 2023 07:37:49 +0000
parents 62fefa284036
children
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line diff
--- a/RM_custom_search.py	Thu Aug 03 10:54:34 2023 +0000
+++ b/RM_custom_search.py	Fri Aug 04 07:37:49 2023 +0000
@@ -57,10 +57,11 @@
 
 def summarizeRepeatMaskerOutput(htmlout = "summary.html"):
     cmd = os.path.dirname(os.path.abspath(__file__))+"/rmsk_summary_table_multiple.r"
-    args = [ cmd, "dir_CL*/reads.fas", "dir_CL*/reads.fas.out", "RM-custom_output_table"  ]
+    args = [ "Rscript", 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]
+    cmd = os.path.dirname(os.path.abspath(__file__))+"/RM_html_report.R"
+    args = ["Rscript", cmd, htmlout]
     status=subprocess.call(args)
     return status