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1 """
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2 Author: Timothy Tickle
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3 Description: Project constants.
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4 """
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5
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6 #####################################################################################
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7 #Copyright (C) <2012>
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8 #
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9 #Permission is hereby granted, free of charge, to any person obtaining a copy of
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10 #this software and associated documentation files (the "Software"), to deal in the
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11 #Software without restriction, including without limitation the rights to use, copy,
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12 #modify, merge, publish, distribute, sublicense, and/or sell copies of the Software,
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13 #and to permit persons to whom the Software is furnished to do so, subject to
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14 #the following conditions:
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15 #
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16 #The above copyright notice and this permission notice shall be included in all copies
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17 #or substantial portions of the Software.
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18 #
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19 #THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
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20 #INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
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21 #PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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22 #HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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23 #OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
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24 #SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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25 #####################################################################################
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26
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27 __author__ = "Timothy Tickle"
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28 __copyright__ = "Copyright 2012"
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29 __credits__ = ["Timothy Tickle"]
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30 __license__ = "MIT"
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31 __maintainer__ = "Timothy Tickle"
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32 __email__ = "ttickle@sph.harvard.edu"
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33 __status__ = "Development"
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34
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35 ##
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36 #Used to test the FileIO class
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37 class ConstantsBreadCrumbs():
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38 """
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39 Class to hold project constants.
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40 """
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41
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42 #Character Constants
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43 c_strComma = ','
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44 c_strColon = ':'
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45 c_strConfigFileHeaderChar = '['
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46 c_strConfigFileCommentChar = '#'
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47 c_strEndline = '\n'
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48 c_strExtDelim = '.'
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49 c_cFastaIDLineStart = '>'
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50 c_strPathDelim = '/'
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51 c_cPipe = '|'
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52 c_cQuote = '\"'
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53 c_cTab = '\t'
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54 c_strWhiteSpace = ' '
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55 c_matrixFileDelim = '\t'
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56
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57 c_strBreadCrumbsSVMSpace = c_strWhiteSpace
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58
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59 #Default values for missing data in the Abundance Table
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60 c_strEmptyAbundanceData = "0"
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61 c_strEmptyDataMetadata = "NA"
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62 c_strSVMNoSample = "-"
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63
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64 lNAs = list(set(["NA","na","Na","nA",c_strEmptyDataMetadata]))
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65
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66 #TODO remove
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67 #Reference to circlader
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68 c_strCircladerScript = "circlader/circlader.py"
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69
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70 #AbundanceTable
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71 #Suffix given to a file that is check with the checkRawDataFile method
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72 OUTPUT_SUFFIX = "-checked.pcl"
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73
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74 #BIOM related
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75 #PCL File metadata defaults (many of these come from biom file requirements
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76 #ID
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77 c_strIDKey = "id"
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78 c_strDefaultPCLID = None
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79
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80 #File date
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81 c_strDateKey = "date"
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82
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83 #File format type
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84 c_strFormatKey = "format"
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85 c_strDefaultPCLFileFormateType = "PCL"
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86
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87 #File generation source
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88 c_strSourceKey = "source"
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89 c_strDefaultPCLGenerationSource = None
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90
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91 #File type
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92 c_strTypekey = "type"
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93 c_strDefaultPCLFileTpe = None
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94
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95 #Allowable file types for biom files
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96 c_strOTUType = "OTU"
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97 c_strOTUBIOMType = "OTU table"
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98 c_strPathwayType = "Pathway"
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99 c_strPathwayBIOMType = "Pathway table"
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100 c_strFunctionType = "Function"
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101 c_strFunctionBIOMType = "Function table"
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102 c_strOrthologType = "Ortholog"
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103 c_strOrthologBIOMType = "Ortholog table"
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104 c_strGeneType = "Gene"
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105 c_strGeneBIOMType = "Gene table"
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106 c_strMetaboliteType = "Metabolite"
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107 c_strMetaboliteBIOMType = "Metabolite table"
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108 c_strTaxonType = "Taxon"
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109 c_strTaxonBIOMType = "Taxon table"
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110 c_dictFileType = {c_strOTUType:c_strOTUBIOMType, c_strPathwayType:c_strPathwayBIOMType, c_strFunctionType:c_strFunctionBIOMType, c_strOrthologType:c_strOrthologBIOMType, c_strGeneType:c_strGeneBIOMType, c_strMetaboliteType:c_strMetaboliteBIOMType, c_strTaxonType:c_strTaxonType}
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111
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112 #File URL
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113 c_strURLKey = "url"
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114 c_strDefaultPCLURL = None
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115 c_strFormatUrl = "format_url"
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116
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117 #File sparse matrix
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118 c_strSparsityKey = "sparsity"
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119 c_fDefaultPCLSparsity = False
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120
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121 # BIOM related Data
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122 # Data shape
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123 c_strDataShapeKey = "shape"
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124
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125 ######################################################################
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126 # Constants related to biom import and export files #
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127 ######################################################################
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128 # Biom file extension
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129 c_strBiomFile = "biom"
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130 c_BiomTaxData = "BiomTaxData"
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131 c_MetadataID = "column_metadata_id"
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132 c_Metadata = "Metadata"
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133 c_metadata_lowercase = "metadata"
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134 c_sLastMetadata = "sLastMetadata"
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135 c_columns = "columns"
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136 c_rows = "rows"
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137 c_ascii = "ascii"
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138 c_ignore = "ignore"
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139 c_Dtype = "Dtype"
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140 c_ID = "ID"
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141 c_id_lowercase = "id"
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142 c_f4 = "f8"
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143 c_biom_file_generated_by = "BreadCrumbs"
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144 c_strPCLFile = "pcl"
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145 c_taxonomy = "taxonomy"
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146 c_dRowsMetadata = "dRowsMetadata"
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147 c_BiomFileInfo = "BiomFileInfo"
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148 c_MatrixTtype = "matrix_type"
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149 c_GeneratedBy = "generated_by"
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150 c_MetadataEntriesTotal = "MetadataEntriesTotal"
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151 c_MaximumLength = "MaximumLength"
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152
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153
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154 def __init__(self):
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155 pass
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