Mercurial > repos > petr-novak > re_utils

comparison RM_custom_search.py @ 14:62fefa284036 draft

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author petr-novak
date Fri, 07 Feb 2020 06:06:47 -0500
parents 16150c85fb3a
children 628b235d76c7
comparison
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13:f12eb3896842 14:62fefa284036
1 #!/usr/bin/env python3 1 #!/usr/bin/env python
2 ''' RepeatMasker search against custom database 2 ''' RepeatMasker search against custom database
3 input: 3 input:
4 - archive with sequencing data 4 - archive with sequencing data
5 - custom repeat database 5 - custom repeat database
6 ''' 6 '''
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, "-f", "dir_CL*/reads.fas", "-r", "dir_CL*/reads.fas.out", "-o", "RM-custom_output_table" ] 60 args = [ cmd, "dir_CL*/reads.fas", "dir_CL*/reads.fas.out", "RM-custom_output_table" ]
61 status=subprocess.call(args) 61 status=subprocess.call(args)
62 cmd = cmd = os.path.dirname(os.path.abspath(__file__))+"/RM_html_report.R" 62 cmd = cmd = os.path.dirname(os.path.abspath(__file__))+"/RM_html_report.R"
63 args = [cmd, htmlout] 63 args = [cmd, htmlout]
64 status=subprocess.call(args) 64 status=subprocess.call(args)
65 return status 65 return status