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7
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1 '''
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2 Containing functions are called from Galaxy to populate lists/checkboxes with selectable items
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3 '''
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4 import csv
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5 import glob
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6 import os
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7
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8
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9 __author__ = "Marcel Kempenaar"
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10 __contact__ = "brs@nbic.nl"
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11 __copyright__ = "Copyright, 2012, Netherlands Bioinformatics Centre"
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12 __license__ = "MIT"
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13
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14 def get_column_type(library_file):
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15 '''
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16 Returns a Galaxy formatted list of tuples containing all possibilities for the
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17 GC-column types. Used by the library_lookup.xml tool
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18 @param library_file: given library file from which the list of GC-column types is extracted
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19 '''
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20 if library_file == "":
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21 galaxy_output = [("", "", False)]
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22 else:
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23 (data, header) = read_library(library_file)
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24
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25 if 'columntype' not in header:
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26 raise IOError('Missing columns in ', library_file)
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27
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28 # Filter data on column type
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29 column_type = header.index("columntype")
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30 amounts_in_list_dict = count_occurrence([row[column_type] for row in data])
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31 galaxy_output = [(str(a) + "(" + str(b) + ")", a, False) for a, b in amounts_in_list_dict.items()]
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32
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33 return(galaxy_output)
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34
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35
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36 def filter_column(library_file, column_type_name):
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37 '''
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38 Filters the Retention Index database on column type
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39 @param library_file: file containing the database
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40 @param column_type_name: column type to filter on
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41 '''
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42 if library_file == "":
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43 galaxy_output = [("", "", False)]
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44 else:
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45 (data, header) = read_library(library_file)
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46
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47 if ('columntype' not in header or
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48 'columnphasetype' not in header):
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49 raise IOError('Missing columns in ', library_file)
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50
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51 column_type = header.index("columntype")
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52 statphase = header.index("columnphasetype")
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53
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54 # Filter data on colunn type name
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55 statphase_list = [line[statphase] for line in data if line[column_type] == column_type_name]
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56 amounts_in_list_dict = count_occurrence(statphase_list)
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57 galaxy_output = [(str(a) + "(" + str(b) + ")", a, False)for a, b in amounts_in_list_dict.items()]
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58
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59 return(sorted(galaxy_output))
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60
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61
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62 def filter_column2(library_file, column_type_name, statphase):
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63 '''
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64 Filters the Retention Index database on column type
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65 @param library_file: file containing the database
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66 @param column_type_name: column type to filter on
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67 @param statphase: stationary phase of the column to filter on
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68 '''
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69 if library_file == "":
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70 galaxy_output = [("", "", False)]
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71 else:
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72 (data, header) = read_library(library_file)
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73
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74 if ('columntype' not in header or
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75 'columnphasetype' not in header or
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76 'columnname' not in header):
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77 raise IOError('Missing columns in ', library_file)
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78
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79 column_type_column = header.index("columntype")
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80 statphase_column = header.index("columnphasetype")
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81 column_name_column = header.index("columnname")
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82
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83 # Filter data on given column type name and stationary phase
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84 statphase_list = [line[column_name_column] for line in data if line[column_type_column] == column_type_name and
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85 line[statphase_column] == statphase]
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86 amounts_in_list_dict = count_occurrence(statphase_list)
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87 galaxy_output = [(str(a) + "(" + str(b) + ")", a, False)for a, b in amounts_in_list_dict.items()]
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88
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89 return(sorted(galaxy_output))
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90
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91
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92 def read_library(filename):
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93 '''
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94 Reads a CSV file and returns its contents and a normalized header
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95 @param filename: file to read
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96 '''
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97 data = list(csv.reader(open(filename, 'rU'), delimiter='\t'))
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98 header_clean = [i.lower().strip().replace(".", "").replace("%", "") for i in data.pop(0)]
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99 return(data, header_clean)
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100
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101
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102
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103 def get_directory_files(dir_name):
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104 '''
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105 Reads the directory and
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106 returns the list of .txt files found as a dictionary
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107 with file name and full path so that it can
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108 fill a Galaxy drop-down combo box.
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109
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110 '''
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111 files = glob.glob(dir_name + "/*.*")
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112 if len(files) == 0:
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113 # Configuration error: no library files found in <galaxy-home-dir>/" + dir_name :
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114 galaxy_output = [("Configuration error: expected file not found in <galaxy-home-dir>/" + dir_name, "", False)]
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115 else:
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116 galaxy_output = [(str(get_file_name_no_ext(file_name)), str(os.path.abspath(file_name)), False) for file_name in files]
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117 return(galaxy_output)
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118
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119 def get_file_name_no_ext(full_name):
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120 '''
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121 returns just the last part of the name
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122 '''
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123 simple_name = os.path.basename(full_name)
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124 base, ext = os.path.splitext(simple_name)
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125 return base
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126
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127
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128 def count_occurrence(data_list):
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129 '''
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130 Counts occurrences in a list and returns a dict with item:occurrence
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131 @param data_list: list to count items from
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132 '''
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133 return dict((key, data_list.count(key)) for key in set(data_list))
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