Mercurial > repos > devteam > table_annovar

comparison replace_NA.py @ 8:d4e292ddda05 draft default tip

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"planemo upload for repository Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
author devteam
date Thu, 05 May 2022 13:13:11 +0000
parents 5cb2020a097a
children
comparison
equal deleted inserted replaced
7:08b003ee9db7 8:d4e292ddda05
61 # Close temp file so that it can be read. 61 # Close temp file so that it can be read.
62 temp_name = temp_out.name 62 temp_name = temp_out.name
63 temp_out.close() 63 temp_out.close()
64 64
65 # Get column type based on label or consensus. 65 # Get column type based on label or consensus.
66 col_types = range(len(col_type_counts)) 66 col_types = list(range(len(col_type_counts)))
67 for i, counts in enumerate(col_type_counts): 67 for i, counts in enumerate(col_type_counts):
68 if i in numerical_cols: 68 if i in numerical_cols:
69 col_type = 'number' 69 col_type = 'number'
70 elif counts[0] > counts[1]: 70 elif counts[0] > counts[1]:
71 col_type = 'string' 71 col_type = 'string'
77 for line in open(temp_name, 'r'): 77 for line in open(temp_name, 'r'):
78 fields = line.strip().split(SEPARATOR) 78 fields = line.strip().split(SEPARATOR)
79 for i, f in enumerate(fields): 79 for i, f in enumerate(fields):
80 if fields[i] == TARGET and col_types[i] == 'number': 80 if fields[i] == TARGET and col_types[i] == 'number':
81 fields[i] = str(REPLACEMENT) 81 fields[i] = str(REPLACEMENT)
82 print SEPARATOR.join(fields) 82 print(SEPARATOR.join(fields))
83 83
84 # Clean up temp file. 84 # Clean up temp file.
85 temp_out.close() 85 temp_out.close()
86 os.unlink(temp_out.name) 86 os.unlink(temp_out.name)
87 87