Mercurial > repos > proteore > proteore_reactome

comparison reactome_analysis.py @ 4:878128362e33 draft

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planemo upload commit 34edf9c3db61650a03d5a0d548b9697a94ecde34-dirty
author proteore
date Tue, 03 Apr 2018 08:24:45 -0400
parents 216bd2a75b1d
children 9cc475dcd0f2
comparison
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3:be06c14e543d 4:878128362e33
21 21
22 def isnumber(format, n): 22 def isnumber(format, n):
23 """ 23 """
24 Check if an variable is numeric 24 Check if an variable is numeric
25 """ 25 """
26 float_format = re.compile("^[\-]?[1-9][0-9]*\.?[0-9]+$") 26 float_format = re.compile(r"^[-]?[1-9][0-9]*.?[0-9]+$")
27 int_format = re.compile("^[\-]?[1-9][0-9]*$") 27 int_format = re.compile(r"^[-]?[1-9][0-9]*$")
28 test = "" 28 test = ""
29 if format == "int": 29 if format == "int":
30 test = re.match(int_format, n) 30 test = re.match(int_format, n)
31 elif format == "float": 31 elif format == "float":
32 test = re.match(float_format, n) 32 test = re.match(float_format, n)
79 except ValueError: 79 except ValueError:
80 output.write("An error occurred due to unavailability of Reactome web service. Please return later.") 80 output.write("An error occurred due to unavailability of Reactome web service. Please return later.")
81 template.close() 81 template.close()
82 output.close() 82 output.close()
83 83
84 trash_out = open(trash_file, "w") 84 if trash:
85 trash_out.write("\n".join(trash)) 85 print(trash)
86 trash_out.close() 86 trash_out = open(trash_file, "w")
87 trash_out.write("\n".join(trash))
88 trash_out.close()
87 89
88 def options(): 90 def options():
89 parser = argparse.ArgumentParser() 91 parser = argparse.ArgumentParser()
90 argument = parser.add_argument("--json", nargs="+", required=True) 92 argument = parser.add_argument("--json", nargs="+", required=True)
91 argument = parser.add_argument("--output", default="output.html") 93 argument = parser.add_argument("--output", default="output.html")