Mercurial > repos > petr-novak > re_utils
comparison RM_custom_search.py @ 32:628b235d76c7 draft
planemo upload commit 39094a128ea3dd2c39f4997c6de739c33c07e5f3-dirty
| author | petr-novak |
|---|---|
| date | Fri, 04 Aug 2023 07:37:49 +0000 |
| parents | 62fefa284036 |
| children |
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| 31:be1f407e1018 | 32:628b235d76c7 |
|---|---|
| 55 status=subprocess.call(args , stderr = open(os.devnull, 'wb')) | 55 status=subprocess.call(args , stderr = open(os.devnull, 'wb')) |
| 56 return status | 56 return status |
| 57 | 57 |
| 58 def summarizeRepeatMaskerOutput(htmlout = "summary.html"): | 58 def summarizeRepeatMaskerOutput(htmlout = "summary.html"): |
| 59 cmd = os.path.dirname(os.path.abspath(__file__))+"/rmsk_summary_table_multiple.r" | 59 cmd = os.path.dirname(os.path.abspath(__file__))+"/rmsk_summary_table_multiple.r" |
| 60 args = [ cmd, "dir_CL*/reads.fas", "dir_CL*/reads.fas.out", "RM-custom_output_table" ] | 60 args = [ "Rscript", cmd, "dir_CL*/reads.fas", "dir_CL*/reads.fas.out", |
| 61 "RM-custom_output_table" ] | |
| 61 status=subprocess.call(args) | 62 status=subprocess.call(args) |
| 62 cmd = cmd = os.path.dirname(os.path.abspath(__file__))+"/RM_html_report.R" | 63 cmd = os.path.dirname(os.path.abspath(__file__))+"/RM_html_report.R" |
| 63 args = [cmd, htmlout] | 64 args = ["Rscript", cmd, htmlout] |
| 64 status=subprocess.call(args) | 65 status=subprocess.call(args) |
| 65 return status | 66 return status |
| 66 | 67 |
| 67 | 68 |
| 68 def main(): | 69 def main(): |