Mercurial > repos > pieterlukasse > prims_metabolomics

comparison match_library.py @ 5:b1d339e0147e

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files in library reader
author pieter.lukasse@wur.nl
date Tue, 21 Jan 2014 15:47:39 +0100
parents 9d5f4f5f764b
children eabfda6213ae
comparison
equal deleted inserted replaced
4:80075a4c6543 5:b1d339e0147e
15 ''' 15 '''
16 Returns a Galaxy formatted list of tuples containing all possibilities for the 16 Returns a Galaxy formatted list of tuples containing all possibilities for the
17 GC-column types. Used by the library_lookup.xml tool 17 GC-column types. Used by the library_lookup.xml tool
18 @param library_file: given library file from which the list of GC-column types is extracted 18 @param library_file: given library file from which the list of GC-column types is extracted
19 ''' 19 '''
20 (data, header) = read_library(library_file) 20 if library_file == "":
21 21 galaxy_output = [("", "", False)]
22 if 'columntype' not in header: 22 else:
23 raise IOError('Missing columns in ', library_file) 23 (data, header) = read_library(library_file)
24 24
25 # Filter data on column type 25 if 'columntype' not in header:
26 column_type = header.index("columntype") 26 raise IOError('Missing columns in ', library_file)
27 amounts_in_list_dict = count_occurrence([row[column_type] for row in data]) 27
28 galaxy_output = [(str(a) + "(" + str(b) + ")", a, False) for a, b in amounts_in_list_dict.items()] 28 # Filter data on column type
29 column_type = header.index("columntype")
30 amounts_in_list_dict = count_occurrence([row[column_type] for row in data])
31 galaxy_output = [(str(a) + "(" + str(b) + ")", a, False) for a, b in amounts_in_list_dict.items()]
32
29 return(galaxy_output) 33 return(galaxy_output)
30 34
31 35
32 def filter_column(library_file, column_type_name): 36 def filter_column(library_file, column_type_name):
33 ''' 37 '''
34 Filters the Retention Index database on column type 38 Filters the Retention Index database on column type
35 @param library_file: file containing the database 39 @param library_file: file containing the database
36 @param column_type_name: column type to filter on 40 @param column_type_name: column type to filter on
37 ''' 41 '''
38 (data, header) = read_library(library_file) 42 if library_file == "":
39 43 galaxy_output = [("", "", False)]
40 if ('columntype' not in header or 44 else:
41 'columnphasetype' not in header): 45 (data, header) = read_library(library_file)
42 raise IOError('Missing columns in ', library_file) 46
43 47 if ('columntype' not in header or
44 column_type = header.index("columntype") 48 'columnphasetype' not in header):
45 statphase = header.index("columnphasetype") 49 raise IOError('Missing columns in ', library_file)
46 50
47 # Filter data on colunn type name 51 column_type = header.index("columntype")
48 statphase_list = [line[statphase] for line in data if line[column_type] == column_type_name] 52 statphase = header.index("columnphasetype")
49 amounts_in_list_dict = count_occurrence(statphase_list) 53
50 galaxy_output = [(str(a) + "(" + str(b) + ")", a, False)for a, b in amounts_in_list_dict.items()] 54 # Filter data on colunn type name
55 statphase_list = [line[statphase] for line in data if line[column_type] == column_type_name]
56 amounts_in_list_dict = count_occurrence(statphase_list)
57 galaxy_output = [(str(a) + "(" + str(b) + ")", a, False)for a, b in amounts_in_list_dict.items()]
58
51 return(sorted(galaxy_output)) 59 return(sorted(galaxy_output))
52 60
53 61
54 def filter_column2(library_file, column_type_name, statphase): 62 def filter_column2(library_file, column_type_name, statphase):
55 ''' 63 '''
56 Filters the Retention Index database on column type 64 Filters the Retention Index database on column type
57 @param library_file: file containing the database 65 @param library_file: file containing the database
58 @param column_type_name: column type to filter on 66 @param column_type_name: column type to filter on
59 @param statphase: stationary phase of the column to filter on 67 @param statphase: stationary phase of the column to filter on
60 ''' 68 '''
61 (data, header) = read_library(library_file) 69 if library_file == "":
62 70 galaxy_output = [("", "", False)]
63 if ('columntype' not in header or 71 else:
64 'columnphasetype' not in header or 72 (data, header) = read_library(library_file)
65 'columnname' not in header): 73
66 raise IOError('Missing columns in ', library_file) 74 if ('columntype' not in header or
67 75 'columnphasetype' not in header or
68 column_type_column = header.index("columntype") 76 'columnname' not in header):
69 statphase_column = header.index("columnphasetype") 77 raise IOError('Missing columns in ', library_file)
70 column_name_column = header.index("columnname") 78
71 79 column_type_column = header.index("columntype")
72 # Filter data on given column type name and stationary phase 80 statphase_column = header.index("columnphasetype")
73 statphase_list = [line[column_name_column] for line in data if line[column_type_column] == column_type_name and 81 column_name_column = header.index("columnname")
74 line[statphase_column] == statphase] 82
75 amounts_in_list_dict = count_occurrence(statphase_list) 83 # Filter data on given column type name and stationary phase
76 galaxy_output = [(str(a) + "(" + str(b) + ")", a, False)for a, b in amounts_in_list_dict.items()] 84 statphase_list = [line[column_name_column] for line in data if line[column_type_column] == column_type_name and
85 line[statphase_column] == statphase]
86 amounts_in_list_dict = count_occurrence(statphase_list)
87 galaxy_output = [(str(a) + "(" + str(b) + ")", a, False)for a, b in amounts_in_list_dict.items()]
88
77 return(sorted(galaxy_output)) 89 return(sorted(galaxy_output))
78 90
79 91
80 def read_library(filename): 92 def read_library(filename):
81 ''' 93 '''
96 fill a Galaxy drop-down combo box. 108 fill a Galaxy drop-down combo box.
97 109
98 ''' 110 '''
99 files = glob.glob(dir_name + "/*.txt") 111 files = glob.glob(dir_name + "/*.txt")
100 if len(files) == 0: 112 if len(files) == 0:
101 raise Exception("Configuration error: no library files found in <galaxy-home-dir>/" + dir_name) 113 # Configuration error: no library files found in <galaxy-home-dir>/" + dir_name :
114 galaxy_output = [("Configuration error: no library files found", "", False)]
102 else: 115 else:
103 galaxy_output = [(str(get_file_name_no_ext(file_name)), str(os.path.abspath(file_name)), False) for file_name in files] 116 galaxy_output = [(str(get_file_name_no_ext(file_name)), str(os.path.abspath(file_name)), False) for file_name in files]
104 return(galaxy_output) 117 return(galaxy_output)
105 118
106 def get_file_name_no_ext(full_name): 119 def get_file_name_no_ext(full_name):