Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/lib/galaxy/datatypes/metagenomics.py @ 30:a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
author | Jim Johnson <jj@umn.edu> |
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date | Thu, 30 May 2013 08:59:17 -0500 |
parents | 9c0cd3b92295 |
children | ec8df51e841a |
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1 """ |
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2 metagenomics datatypes |
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3 James E Johnson - University of Minnesota |
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4 for Mothur |
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5 """ |
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6 |
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7 import logging, os, os.path, sys, time, tempfile, shutil, string, glob, re |
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8 import galaxy.model |
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9 from galaxy.datatypes.sniff import * |
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10 from galaxy.datatypes.metadata import MetadataElement |
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11 from galaxy.datatypes.data import Text |
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12 from galaxy.datatypes.tabular import Tabular |
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13 from galaxy.datatypes.sequence import Fasta |
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14 from galaxy import util |
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15 from galaxy.datatypes.images import Html |
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16 import pkg_resources |
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17 pkg_resources.require("simplejson") |
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18 import simplejson |
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19 |
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20 log = logging.getLogger(__name__) |
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21 |
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22 ## Mothur Classes |
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23 |
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24 class Otu( Text ): |
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25 file_ext = 'otu' |
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26 MetadataElement( name="columns", default=0, desc="Number of columns", readonly=True, visible=True, no_value=0 ) |
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27 MetadataElement( name="labels", default=[], desc="Label Names", readonly=True, visible=True, no_value=[] ) |
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28 def __init__(self, **kwd): |
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29 Text.__init__( self, **kwd ) |
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30 def set_meta( self, dataset, overwrite = True, **kwd ): |
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31 if dataset.has_data(): |
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32 label_names = set() |
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33 ncols = 0 |
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34 data_lines = 0 |
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35 comment_lines = 0 |
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36 try: |
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37 fh = open( dataset.file_name ) |
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38 for line in fh: |
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39 fields = line.strip().split('\t') |
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40 if len(fields) >= 2: |
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41 data_lines += 1 |
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42 ncols = max(ncols,len(fields)) |
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43 label_names.add(fields[0]) |
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44 else: |
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45 comment_lines += 1 |
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46 # Set the discovered metadata values for the dataset |
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47 dataset.metadata.data_lines = data_lines |
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48 dataset.metadata.columns = ncols |
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49 dataset.metadata.labels = [] |
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50 dataset.metadata.labels += label_names |
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51 dataset.metadata.labels.sort() |
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52 finally: |
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53 fh.close() |
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54 |
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55 def sniff( self, filename ): |
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56 """ |
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57 Determines whether the file is a otu (operational taxonomic unit) format |
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58 """ |
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59 try: |
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60 fh = open( filename ) |
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61 count = 0 |
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62 while True: |
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63 line = fh.readline() |
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64 line = line.strip() |
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65 if not line: |
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66 break #EOF |
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67 if line: |
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68 if line[0] != '@': |
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69 linePieces = line.split('\t') |
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70 if len(linePieces) < 2: |
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71 return False |
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72 try: |
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73 check = int(linePieces[1]) |
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74 if check + 2 != len(linePieces): |
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75 return False |
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76 except ValueError: |
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77 return False |
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78 count += 1 |
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79 if count == 5: |
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80 return True |
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81 fh.close() |
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82 if count < 5 and count > 0: |
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83 return True |
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84 except: |
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85 pass |
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86 finally: |
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87 fh.close() |
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88 return False |
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89 |
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90 class OtuList( Otu ): |
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91 file_ext = 'list' |
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92 def __init__(self, **kwd): |
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93 """ |
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94 # http://www.mothur.org/wiki/List_file |
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95 The first column is a label that represents the distance that sequences were assigned to OTUs. |
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96 The number in the second column is the number of OTUs that have been formed. |
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97 Subsequent columns contain the names of sequences within each OTU separated by a comma. |
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98 distance_label otu_count OTU1 OTU2 OTUn |
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99 """ |
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100 Otu.__init__( self, **kwd ) |
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101 def init_meta( self, dataset, copy_from=None ): |
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102 Otu.init_meta( self, dataset, copy_from=copy_from ) |
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103 def set_meta( self, dataset, overwrite = True, **kwd ): |
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104 Otu.set_meta(self,dataset, overwrite = True, **kwd ) |
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105 """ |
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106 # too many columns to be stored in metadata |
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107 if dataset != None and dataset.metadata.columns > 2: |
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108 for i in range(2,dataset.metadata.columns): |
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109 dataset.metadata.column_types[i] = 'str' |
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110 """ |
0
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111 |
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112 class Sabund( Otu ): |
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113 file_ext = 'sabund' |
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114 def __init__(self, **kwd): |
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115 """ |
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116 # http://www.mothur.org/wiki/Sabund_file |
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117 """ |
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118 Otu.__init__( self, **kwd ) |
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119 def init_meta( self, dataset, copy_from=None ): |
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120 Otu.init_meta( self, dataset, copy_from=copy_from ) |
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121 def sniff( self, filename ): |
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122 """ |
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123 Determines whether the file is a otu (operational taxonomic unit) format |
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124 label<TAB>count[<TAB>value(1..n)] |
7 | 125 |
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126 """ |
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127 try: |
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128 fh = open( filename ) |
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129 count = 0 |
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130 while True: |
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131 line = fh.readline() |
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132 line = line.strip() |
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133 if not line: |
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134 break #EOF |
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135 if line: |
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136 if line[0] != '@': |
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137 linePieces = line.split('\t') |
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138 if len(linePieces) < 2: |
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139 return False |
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140 try: |
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141 check = int(linePieces[1]) |
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142 if check + 2 != len(linePieces): |
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143 return False |
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144 for i in range( 2, len(linePieces)): |
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145 ival = int(linePieces[i]) |
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146 except ValueError: |
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147 return False |
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148 count += 1 |
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149 if count >= 5: |
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150 return True |
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151 fh.close() |
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152 if count < 5 and count > 0: |
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153 return True |
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154 except: |
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155 pass |
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156 finally: |
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157 fh.close() |
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158 return False |
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159 |
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160 class Rabund( Sabund ): |
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161 file_ext = 'rabund' |
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162 def __init__(self, **kwd): |
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163 """ |
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164 # http://www.mothur.org/wiki/Rabund_file |
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165 """ |
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166 Sabund.__init__( self, **kwd ) |
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167 def init_meta( self, dataset, copy_from=None ): |
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168 Sabund.init_meta( self, dataset, copy_from=copy_from ) |
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169 |
7 | 170 class GroupAbund( Otu ): |
171 file_ext = 'grpabund' | |
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172 MetadataElement( name="groups", default=[], desc="Group Names", readonly=True, visible=True, no_value=[] ) |
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173 def __init__(self, **kwd): |
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174 Otu.__init__( self, **kwd ) |
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175 # self.column_names[0] = ['label'] |
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176 # self.column_names[1] = ['group'] |
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177 # self.column_names[2] = ['count'] |
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178 """ |
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179 def init_meta( self, dataset, copy_from=None ): |
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180 Otu.init_meta( self, dataset, copy_from=copy_from ) |
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181 """ |
7 | 182 def init_meta( self, dataset, copy_from=None ): |
183 Otu.init_meta( self, dataset, copy_from=copy_from ) | |
184 def set_meta( self, dataset, overwrite = True, skip=1, max_data_lines = 100000, **kwd ): | |
185 # See if file starts with header line | |
186 if dataset.has_data(): | |
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187 label_names = set() |
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188 group_names = set() |
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189 data_lines = 0 |
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190 comment_lines = 0 |
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191 ncols = 0 |
7 | 192 try: |
193 fh = open( dataset.file_name ) | |
194 line = fh.readline() | |
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195 fields = line.strip().split('\t') |
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196 ncols = max(ncols,len(fields)) |
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197 if fields[0] == 'label' and fields[1] == 'Group': |
7 | 198 skip=1 |
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199 comment_lines += 1 |
7 | 200 else: |
201 skip=0 | |
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202 data_lines += 1 |
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203 label_names.add(fields[0]) |
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204 group_names.add(fields[1]) |
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205 for line in fh: |
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206 data_lines += 1 |
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207 fields = line.strip().split('\t') |
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208 ncols = max(ncols,len(fields)) |
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209 label_names.add(fields[0]) |
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210 group_names.add(fields[1]) |
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211 # Set the discovered metadata values for the dataset |
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212 dataset.metadata.data_lines = data_lines |
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213 dataset.metadata.columns = ncols |
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214 dataset.metadata.labels = [] |
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215 dataset.metadata.labels += label_names |
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216 dataset.metadata.labels.sort() |
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217 dataset.metadata.groups = [] |
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218 dataset.metadata.groups += group_names |
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219 dataset.metadata.groups.sort() |
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220 dataset.metadata.skip = skip |
7 | 221 finally: |
222 fh.close() | |
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223 |
7 | 224 def sniff( self, filename, vals_are_int=False): |
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225 """ |
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226 Determines whether the file is a otu (operational taxonomic unit) Shared format |
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227 label<TAB>group<TAB>count[<TAB>value(1..n)] |
7 | 228 The first line is column headings as of Mothur v 1.20 |
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229 """ |
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230 try: |
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231 fh = open( filename ) |
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232 count = 0 |
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233 while True: |
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234 line = fh.readline() |
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235 line = line.strip() |
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236 if not line: |
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237 break #EOF |
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238 if line: |
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239 if line[0] != '@': |
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240 linePieces = line.split('\t') |
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241 if len(linePieces) < 3: |
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242 return False |
7 | 243 if count > 0 or linePieces[0] != 'label': |
244 try: | |
245 check = int(linePieces[2]) | |
246 if check + 3 != len(linePieces): | |
247 return False | |
248 for i in range( 3, len(linePieces)): | |
249 if vals_are_int: | |
250 ival = int(linePieces[i]) | |
251 else: | |
252 fval = float(linePieces[i]) | |
253 except ValueError: | |
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254 return False |
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255 count += 1 |
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256 if count >= 5: |
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257 return True |
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258 fh.close() |
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259 if count < 5 and count > 0: |
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260 return True |
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261 except: |
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262 pass |
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263 finally: |
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264 fh.close() |
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265 return False |
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266 |
7 | 267 class SharedRabund( GroupAbund ): |
268 file_ext = 'shared' | |
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269 def __init__(self, **kwd): |
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270 """ |
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271 # http://www.mothur.org/wiki/Shared_file |
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272 A shared file is analogous to an rabund file. |
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273 The data in a shared file represent the number of times that an OTU is observed in multiple samples. |
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274 The structure of a shared file is analogous to an rabund file. |
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275 The first column contains the label for the comparison - this will be the value for the first column of each line from the original list file. |
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276 The second column contains the group name that designates where the data is coming from for that row. |
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277 The third column is the number of OTUs that were found between each of the groups and is the number of columns that follow. |
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278 Finally, the remaining columns indicate the number of sequences that belonged to each OTU from that group. |
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279 """ |
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280 GroupAbund.__init__( self, **kwd ) |
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281 def init_meta( self, dataset, copy_from=None ): |
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282 GroupAbund.init_meta( self, dataset, copy_from=copy_from ) |
7 | 283 def sniff( self, filename ): |
284 """ | |
285 Determines whether the file is a otu (operational taxonomic unit) Shared format | |
286 label<TAB>group<TAB>count[<TAB>value(1..n)] | |
287 The first line is column headings as of Mothur v 1.20 | |
288 """ | |
289 # return GroupAbund.sniff(self,filename,True) | |
290 isme = GroupAbund.sniff(self,filename,True) | |
291 return isme | |
292 | |
293 | |
294 class RelAbund( GroupAbund ): | |
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295 file_ext = 'relabund' |
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296 def __init__(self, **kwd): |
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297 """ |
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298 # http://www.mothur.org/wiki/Relabund_file |
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299 The structure of a relabund file is analogous to an shared file. |
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300 The first column contains the label for the comparison - this will be the value for the first column of each line from the original list file (e.g. final.an.list). |
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301 The second column contains the group name that designates where the data is coming from for that row. Next is the number of OTUs that were found between each of the groups and is the number of columns that follow. |
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302 Finally, the remaining columns indicate the relative abundance of each OTU from that group. |
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303 """ |
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304 GroupAbund.__init__( self, **kwd ) |
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305 def init_meta( self, dataset, copy_from=None ): |
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306 GroupAbund.init_meta( self, dataset, copy_from=copy_from ) |
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307 def sniff( self, filename ): |
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308 """ |
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309 Determines whether the file is a otu (operational taxonomic unit) Relative Abundance format |
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310 label<TAB>group<TAB>count[<TAB>value(1..n)] |
7 | 311 The first line is column headings as of Mothur v 1.20 |
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312 """ |
7 | 313 # return GroupAbund.sniff(self,filename,False) |
314 isme = GroupAbund.sniff(self,filename,False) | |
315 return isme | |
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316 |
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317 class SecondaryStructureMap(Tabular): |
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318 file_ext = 'map' |
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319 def __init__(self, **kwd): |
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320 """Initialize secondary structure map datatype""" |
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321 Tabular.__init__( self, **kwd ) |
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322 self.column_names = ['Map'] |
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323 |
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324 def sniff( self, filename ): |
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325 """ |
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326 Determines whether the file is a secondary structure map format |
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327 A single column with an integer value which indicates the row that this row maps to. |
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328 check you make sure is structMap[10] = 380 then structMap[380] = 10. |
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329 """ |
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330 try: |
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331 fh = open( filename ) |
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332 line_num = 0 |
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333 rowidxmap = {} |
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334 while True: |
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335 line = fh.readline() |
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336 line_num += 1 |
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337 line = line.strip() |
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338 if not line: |
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339 break #EOF |
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340 if line: |
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341 try: |
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342 pointer = int(line) |
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343 if pointer > 0: |
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344 if pointer > line_num: |
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345 rowidxmap[line_num] = pointer |
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346 elif pointer < line_num & rowidxmap[pointer] != line_num: |
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347 return False |
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348 except ValueError: |
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349 return False |
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350 fh.close() |
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351 if count < 5 and count > 0: |
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352 return True |
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353 except: |
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354 pass |
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355 finally: |
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356 fh.close() |
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357 return False |
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358 |
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359 class SequenceAlignment( Fasta ): |
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360 file_ext = 'align' |
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361 def __init__(self, **kwd): |
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362 Fasta.__init__( self, **kwd ) |
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363 """Initialize AlignCheck datatype""" |
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364 |
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365 def sniff( self, filename ): |
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366 """ |
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367 Determines whether the file is in Mothur align fasta format |
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368 Each sequence line must be the same length |
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369 """ |
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370 |
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371 try: |
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372 fh = open( filename ) |
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373 len = -1 |
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374 while True: |
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375 line = fh.readline() |
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376 if not line: |
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377 break #EOF |
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378 line = line.strip() |
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379 if line: #first non-empty line |
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380 if line.startswith( '>' ): |
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381 #The next line.strip() must not be '', nor startwith '>' |
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382 line = fh.readline().strip() |
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383 if line == '' or line.startswith( '>' ): |
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384 break |
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385 if len < 0: |
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386 len = len(line) |
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387 elif len != len(line): |
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388 return False |
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389 else: |
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390 break #we found a non-empty line, but its not a fasta header |
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391 if len > 0: |
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392 return True |
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393 except: |
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394 pass |
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395 finally: |
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396 fh.close() |
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397 return False |
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398 |
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399 class AlignCheck( Tabular ): |
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400 file_ext = 'align.check' |
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401 def __init__(self, **kwd): |
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402 """Initialize AlignCheck datatype""" |
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403 Tabular.__init__( self, **kwd ) |
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404 self.column_names = ['name','pound','dash','plus','equal','loop','tilde','total'] |
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405 self.column_types = ['str','int','int','int','int','int','int','int'] |
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406 self.comment_lines = 1 |
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407 |
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408 def set_meta( self, dataset, overwrite = True, **kwd ): |
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409 # Tabular.set_meta( self, dataset, overwrite = overwrite, first_line_is_header = True, skip = 1 ) |
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410 data_lines = 0 |
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411 if dataset.has_data(): |
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412 dataset_fh = open( dataset.file_name ) |
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413 while True: |
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414 line = dataset_fh.readline() |
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415 if not line: break |
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416 data_lines += 1 |
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417 dataset_fh.close() |
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418 dataset.metadata.comment_lines = 1 |
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419 dataset.metadata.data_lines = data_lines - 1 if data_lines > 0 else 0 |
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420 dataset.metadata.column_names = self.column_names |
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421 dataset.metadata.column_types = self.column_types |
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422 |
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423 class AlignReport(Tabular): |
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424 """ |
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425 QueryName QueryLength TemplateName TemplateLength SearchMethod SearchScore AlignmentMethod QueryStart QueryEnd TemplateStart TemplateEnd PairwiseAlignmentLength GapsInQuery GapsInTemplate LongestInsert SimBtwnQuery&Template |
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426 AY457915 501 82283 1525 kmer 89.07 needleman 5 501 1 499 499 2 0 0 97.6 |
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427 """ |
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428 file_ext = 'align.report' |
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429 def __init__(self, **kwd): |
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430 """Initialize AlignCheck datatype""" |
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431 Tabular.__init__( self, **kwd ) |
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432 self.column_names = ['QueryName','QueryLength','TemplateName','TemplateLength','SearchMethod','SearchScore', |
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433 'AlignmentMethod','QueryStart','QueryEnd','TemplateStart','TemplateEnd', |
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434 'PairwiseAlignmentLength','GapsInQuery','GapsInTemplate','LongestInsert','SimBtwnQuery&Template' |
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|
435 ] |
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changeset
|
436 |
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|
437 class BellerophonChimera( Tabular ): |
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438 file_ext = 'bellerophon.chimera' |
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439 def __init__(self, **kwd): |
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440 """Initialize AlignCheck datatype""" |
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|
441 Tabular.__init__( self, **kwd ) |
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442 self.column_names = ['Name','Score','Left','Right'] |
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|
443 |
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|
444 class SecondaryStructureMatch(Tabular): |
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diff
changeset
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445 """ |
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446 name pound dash plus equal loop tilde total |
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diff
changeset
|
447 9_1_12 42 68 8 28 275 420 872 |
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diff
changeset
|
448 9_1_14 36 68 6 26 266 422 851 |
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jjohnson
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diff
changeset
|
449 9_1_15 44 68 8 28 276 418 873 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff
changeset
|
450 9_1_16 34 72 6 30 267 430 860 |
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jjohnson
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diff
changeset
|
451 9_1_18 46 80 2 36 261 |
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jjohnson
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452 """ |
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453 def __init__(self, **kwd): |
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changeset
|
454 """Initialize SecondaryStructureMatch datatype""" |
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455 Tabular.__init__( self, **kwd ) |
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456 self.column_names = ['name','pound','dash','plus','equal','loop','tilde','total'] |
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diff
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|
457 |
17
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
458 class DistanceMatrix( Text ): |
0
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459 file_ext = 'dist' |
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460 """Add metadata elements""" |
25
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
461 MetadataElement( name="sequence_count", default=0, desc="Number of sequences", readonly=True, visible=True, optional=True, no_value='?' ) |
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
462 |
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
463 def init_meta( self, dataset, copy_from=None ): |
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
464 Text.init_meta( self, dataset, copy_from=copy_from ) |
0
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parents:
diff
changeset
|
465 |
25
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
466 def set_meta( self, dataset, overwrite = True, skip = 0, **kwd ): |
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Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
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17
diff
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|
467 Text.set_meta(self, dataset,overwrite = overwrite, skip = skip, **kwd ) |
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Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
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|
468 try: |
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
469 fh = open( dataset.file_name ) |
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
470 line = fh.readline().strip().strip() |
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
471 dataset.metadata.sequence_count = int(line) |
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
472 except Exception, e: |
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
473 log.warn("DistanceMatrix set_meta %s" % e) |
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
474 finally: |
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
475 fh.close() |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
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diff
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|
476 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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changeset
|
477 class LowerTriangleDistanceMatrix(DistanceMatrix): |
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Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff
changeset
|
478 file_ext = 'lower.dist' |
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Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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diff
changeset
|
479 def __init__(self, **kwd): |
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Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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changeset
|
480 """Initialize secondary structure map datatype""" |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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changeset
|
481 DistanceMatrix.__init__( self, **kwd ) |
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Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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changeset
|
482 |
25
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
483 def init_meta( self, dataset, copy_from=None ): |
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
484 DistanceMatrix.init_meta( self, dataset, copy_from=copy_from ) |
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
485 |
0
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Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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|
486 def sniff( self, filename ): |
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Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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changeset
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487 """ |
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Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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changeset
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488 Determines whether the file is a lower-triangle distance matrix (phylip) format |
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Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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489 The first line has the number of sequences in the matrix. |
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Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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490 The remaining lines have the sequence name followed by a list of distances from all preceeding sequences |
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Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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491 5 |
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Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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changeset
|
492 U68589 |
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Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
493 U68590 0.3371 |
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Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
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changeset
|
494 U68591 0.3609 0.3782 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
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changeset
|
495 U68592 0.4155 0.3197 0.4148 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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changeset
|
496 U68593 0.2872 0.1690 0.3361 0.2842 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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changeset
|
497 """ |
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498 try: |
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499 fh = open( filename ) |
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Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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changeset
|
500 count = 0 |
29
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
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diff
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|
501 line = fh.readline() |
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Fixes for metagenomics.py datatypes tahnks to Peter Briggs
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27
diff
changeset
|
502 sequence_count = int(line.strip()) |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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|
503 while True: |
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Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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changeset
|
504 line = fh.readline() |
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Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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parents:
diff
changeset
|
505 line = line.strip() |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
506 if not line: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
507 break #EOF |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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changeset
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508 if line: |
29
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
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diff
changeset
|
509 # Split into fields |
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
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parents:
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diff
changeset
|
510 linePieces = line.split('\t') |
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
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parents:
27
diff
changeset
|
511 # Each line should have the same number of |
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
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diff
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|
512 # fields as the Python line index |
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
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diff
changeset
|
513 linePieces = line.split('\t') |
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
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27
diff
changeset
|
514 if len(linePieces) != (count + 1): |
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
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diff
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|
515 return False |
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Fixes for metagenomics.py datatypes tahnks to Peter Briggs
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parents:
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diff
changeset
|
516 # Distances should be floats |
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
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parents:
27
diff
changeset
|
517 try: |
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
Jim Johnson <jj@umn.edu>
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27
diff
changeset
|
518 for linePiece in linePieces[2:]: |
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
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27
diff
changeset
|
519 check = float(linePiece) |
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Fixes for metagenomics.py datatypes tahnks to Peter Briggs
Jim Johnson <jj@umn.edu>
parents:
27
diff
changeset
|
520 except ValueError: |
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
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parents:
27
diff
changeset
|
521 return False |
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
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parents:
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diff
changeset
|
522 # Increment line counter |
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
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27
diff
changeset
|
523 count += 1 |
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
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parents:
27
diff
changeset
|
524 # Only check first 5 lines |
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
Jim Johnson <jj@umn.edu>
parents:
27
diff
changeset
|
525 if count == 5: |
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
Jim Johnson <jj@umn.edu>
parents:
27
diff
changeset
|
526 return True |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
527 fh.close() |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
528 if count < 5 and count > 0: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
529 return True |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
530 except: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
531 pass |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
532 finally: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
533 fh.close() |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
534 return False |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
535 |
25
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
536 class SquareDistanceMatrix(DistanceMatrix): |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
537 file_ext = 'square.dist' |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
538 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
539 def __init__(self, **kwd): |
25
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
540 DistanceMatrix.__init__( self, **kwd ) |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
541 def init_meta( self, dataset, copy_from=None ): |
25
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
542 DistanceMatrix.init_meta( self, dataset, copy_from=copy_from ) |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
543 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
544 def sniff( self, filename ): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
545 """ |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
546 Determines whether the file is a square distance matrix (Column-formatted distance matrix) format |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
547 The first line has the number of sequences in the matrix. |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
548 The following lines have the sequence name in the first column plus a column for the distance to each sequence |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
549 in the row order in which they appear in the matrix. |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
550 3 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
551 U68589 0.0000 0.3371 0.3610 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
552 U68590 0.3371 0.0000 0.3783 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
553 U68590 0.3371 0.0000 0.3783 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
554 """ |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
555 try: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
556 fh = open( filename ) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
557 count = 0 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
558 line = fh.readline() |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
559 line = line.strip() |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
560 sequence_count = int(line) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
561 col_cnt = seq_cnt + 1 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
562 while True: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
563 line = fh.readline() |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
564 line = line.strip() |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
565 if not line: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
566 break #EOF |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
567 if line: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
568 if line[0] != '@': |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
569 linePieces = line.split('\t') |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
570 if len(linePieces) != col_cnt : |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
571 return False |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
572 try: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
573 for i in range(1, col_cnt): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
574 check = float(linePieces[i]) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
575 except ValueError: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
576 return False |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
577 count += 1 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
578 if count == 5: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
579 return True |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
580 fh.close() |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
581 if count < 5 and count > 0: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
582 return True |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
583 except: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
584 pass |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
585 finally: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
586 fh.close() |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
587 return False |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
588 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
589 class PairwiseDistanceMatrix(DistanceMatrix,Tabular): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
590 file_ext = 'pair.dist' |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
591 def __init__(self, **kwd): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
592 """Initialize secondary structure map datatype""" |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
593 Tabular.__init__( self, **kwd ) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
594 self.column_names = ['Sequence','Sequence','Distance'] |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
595 self.column_types = ['str','str','float'] |
25
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
596 def set_meta( self, dataset, overwrite = True, skip = None, **kwd ): |
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
597 Tabular.set_meta(self, dataset,overwrite = overwrite, skip = skip, **kwd ) |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
598 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
599 def sniff( self, filename ): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
600 """ |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
601 Determines whether the file is a pairwise distance matrix (Column-formatted distance matrix) format |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
602 The first and second columns have the sequence names and the third column is the distance between those sequences. |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
603 """ |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
604 try: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
605 fh = open( filename ) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
606 count = 0 |
29
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
Jim Johnson <jj@umn.edu>
parents:
27
diff
changeset
|
607 all_ints = True |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
608 while True: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
609 line = fh.readline() |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
610 line = line.strip() |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
611 if not line: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
612 break #EOF |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
613 if line: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
614 if line[0] != '@': |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
615 linePieces = line.split('\t') |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
616 if len(linePieces) != 3: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
617 return False |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
618 try: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
619 check = float(linePieces[2]) |
29
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
Jim Johnson <jj@umn.edu>
parents:
27
diff
changeset
|
620 try: |
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
Jim Johnson <jj@umn.edu>
parents:
27
diff
changeset
|
621 # See if it's also an integer |
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
Jim Johnson <jj@umn.edu>
parents:
27
diff
changeset
|
622 check_int = int(linePieces[2]) |
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
Jim Johnson <jj@umn.edu>
parents:
27
diff
changeset
|
623 except ValueError: |
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
Jim Johnson <jj@umn.edu>
parents:
27
diff
changeset
|
624 # At least one value is not an |
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
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parents:
27
diff
changeset
|
625 # integer |
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
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parents:
27
diff
changeset
|
626 all_ints = False |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
627 except ValueError: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
628 return False |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
629 count += 1 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
630 if count == 5: |
29
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
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parents:
27
diff
changeset
|
631 if not all_ints: |
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
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parents:
27
diff
changeset
|
632 return True |
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
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parents:
27
diff
changeset
|
633 else: |
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
Jim Johnson <jj@umn.edu>
parents:
27
diff
changeset
|
634 return False |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
635 fh.close() |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
636 if count < 5 and count > 0: |
29
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
Jim Johnson <jj@umn.edu>
parents:
27
diff
changeset
|
637 if not all_ints: |
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
Jim Johnson <jj@umn.edu>
parents:
27
diff
changeset
|
638 return True |
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
Jim Johnson <jj@umn.edu>
parents:
27
diff
changeset
|
639 else: |
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
Jim Johnson <jj@umn.edu>
parents:
27
diff
changeset
|
640 return False |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
641 except: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
642 pass |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
643 finally: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
644 fh.close() |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
645 return False |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
646 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
647 class AlignCheck(Tabular): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
648 file_ext = 'align.check' |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
649 def __init__(self, **kwd): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
650 """Initialize secondary structure map datatype""" |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
651 Tabular.__init__( self, **kwd ) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
652 self.column_names = ['name','pound','dash','plus','equal','loop','tilde','total'] |
1
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
653 self.columns = 8 |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
654 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
655 class Names(Tabular): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
656 file_ext = 'names' |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
657 def __init__(self, **kwd): |
30
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
658 """ |
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
659 # http://www.mothur.org/wiki/Name_file |
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
660 Name file shows the relationship between a representative sequence(col 1) and the sequences(comma-separated) it represents(col 2) |
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
661 """ |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
662 Tabular.__init__( self, **kwd ) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
663 self.column_names = ['name','representatives'] |
1
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
664 self.columns = 2 |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
665 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
666 class Summary(Tabular): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
667 file_ext = 'summary' |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
668 def __init__(self, **kwd): |
1
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
669 """summarizes the quality of sequences in an unaligned or aligned fasta-formatted sequence file""" |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
670 Tabular.__init__( self, **kwd ) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
671 self.column_names = ['seqname','start','end','nbases','ambigs','polymer'] |
1
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
672 self.columns = 6 |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
673 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
674 class Group(Tabular): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
675 file_ext = 'groups' |
25
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
676 MetadataElement( name="groups", default=[], desc="Group Names", readonly=True, visible=True, no_value=[] ) |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
677 def __init__(self, **kwd): |
30
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
678 """ |
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
679 # http://www.mothur.org/wiki/Groups_file |
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
680 Group file assigns sequence (col 1) to a group (col 2) |
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
681 """ |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
682 Tabular.__init__( self, **kwd ) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
683 self.column_names = ['name','group'] |
1
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
684 self.columns = 2 |
25
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
685 def set_meta( self, dataset, overwrite = True, skip = None, max_data_lines = None, **kwd ): |
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
686 Tabular.set_meta(self, dataset, overwrite, skip, max_data_lines) |
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
687 group_names = set() |
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
688 try: |
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
689 fh = open( dataset.file_name ) |
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
690 for line in fh: |
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
691 fields = line.strip().split('\t') |
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
692 group_names.add(fields[1]) |
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
693 dataset.metadata.groups = [] |
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
694 dataset.metadata.groups += group_names |
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
695 finally: |
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
696 fh.close() |
1
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
697 |
25
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
698 class Design(Group): |
1
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
699 file_ext = 'design' |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
700 def __init__(self, **kwd): |
30
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
701 """ |
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
702 # http://www.mothur.org/wiki/Design_File |
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
703 Design file shows the relationship between a group(col 1) and a grouping (col 2), providing a way to merge groups. |
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
704 """ |
25
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
17
diff
changeset
|
705 Group.__init__( self, **kwd ) |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
706 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
707 class AccNos(Tabular): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
708 file_ext = 'accnos' |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
709 def __init__(self, **kwd): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
710 """A list of names""" |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
711 Tabular.__init__( self, **kwd ) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
712 self.column_names = ['name'] |
1
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
713 self.columns = 1 |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
714 |
17
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
715 class Oligos( Text ): |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
716 file_ext = 'oligos' |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
717 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
718 def sniff( self, filename ): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
719 """ |
30
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
720 # http://www.mothur.org/wiki/Oligos_File |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
721 Determines whether the file is a otu (operational taxonomic unit) format |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
722 """ |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
723 try: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
724 fh = open( filename ) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
725 count = 0 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
726 while True: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
727 line = fh.readline() |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
728 line = line.strip() |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
729 if not line: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
730 break #EOF |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
731 else: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
732 if line[0] != '#': |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
733 linePieces = line.split('\t') |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
734 if len(linePieces) == 2 and re.match('forward|reverse',linePieces[0]): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
735 count += 1 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
736 continue |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
737 elif len(linePieces) == 3 and re.match('barcode',linePieces[0]): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
738 count += 1 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
739 continue |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
740 else: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
741 return False |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
742 if count > 20: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
743 return True |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
744 if count > 0: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
745 return True |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
746 except: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
747 pass |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
748 finally: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
749 fh.close() |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
750 return False |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
751 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
752 class Frequency(Tabular): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
753 file_ext = 'freq' |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
754 def __init__(self, **kwd): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
755 """A list of names""" |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
756 Tabular.__init__( self, **kwd ) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
757 self.column_names = ['position','frequency'] |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
758 self.column_types = ['int','float'] |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
759 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
760 def sniff( self, filename ): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
761 """ |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
762 Determines whether the file is a frequency tabular format for chimera analysis |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
763 #1.14.0 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
764 0 0.000 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
765 1 0.000 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
766 ... |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
767 155 0.975 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
768 """ |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
769 try: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
770 fh = open( filename ) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
771 count = 0 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
772 while True: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
773 line = fh.readline() |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
774 line = line.strip() |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
775 if not line: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
776 break #EOF |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
777 else: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
778 if line[0] != '#': |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
779 try: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
780 linePieces = line.split('\t') |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
781 i = int(linePieces[0]) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
782 f = float(linePieces[1]) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
783 count += 1 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
784 continue |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
785 except: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
786 return False |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
787 if count > 20: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
788 return True |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
789 if count > 0: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
790 return True |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
791 except: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
792 pass |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
793 finally: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
794 fh.close() |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
795 return False |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
796 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
797 class Quantile(Tabular): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
798 file_ext = 'quan' |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
799 MetadataElement( name="filtered", default=False, no_value=False, optional=True , desc="Quantiles calculated using a mask", readonly=True) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
800 MetadataElement( name="masked", default=False, no_value=False, optional=True , desc="Quantiles calculated using a frequency filter", readonly=True) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
801 def __init__(self, **kwd): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
802 """Quantiles for chimera analysis""" |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
803 Tabular.__init__( self, **kwd ) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
804 self.column_names = ['num','ten','twentyfive','fifty','seventyfive','ninetyfive','ninetynine'] |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
805 self.column_types = ['int','float','float','float','float','float','float'] |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
806 def sniff( self, filename ): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
807 """ |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
808 Determines whether the file is a quantiles tabular format for chimera analysis |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
809 1 0 0 0 0 0 0 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
810 2 0.309198 0.309198 0.37161 0.37161 0.37161 0.37161 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
811 3 0.510982 0.563213 0.693529 0.858939 1.07442 1.20608 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
812 ... |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
813 """ |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
814 try: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
815 fh = open( filename ) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
816 count = 0 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
817 while True: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
818 line = fh.readline() |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
819 line = line.strip() |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
820 if not line: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
821 break #EOF |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
822 else: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
823 if line[0] != '#': |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
824 try: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
825 linePieces = line.split('\t') |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
826 i = int(linePieces[0]) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
827 f = float(linePieces[1]) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
828 f = float(linePieces[2]) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
829 f = float(linePieces[3]) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
830 f = float(linePieces[4]) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
831 f = float(linePieces[5]) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
832 f = float(linePieces[6]) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
833 count += 1 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
834 continue |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
835 except: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
836 return False |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
837 if count > 10: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
838 return True |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
839 if count > 0: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
840 return True |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
841 except: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
842 pass |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
843 finally: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
844 fh.close() |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
845 return False |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
846 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
847 class FilteredQuantile(Quantile): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
848 file_ext = 'filtered.quan' |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
849 def __init__(self, **kwd): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
850 """Quantiles for chimera analysis""" |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
851 Quantile.__init__( self, **kwd ) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
852 self.filtered = True |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
853 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
854 class MaskedQuantile(Quantile): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
855 file_ext = 'masked.quan' |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
856 def __init__(self, **kwd): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
857 """Quantiles for chimera analysis""" |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
858 Quantile.__init__( self, **kwd ) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
859 self.masked = True |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
860 self.filtered = False |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
861 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
862 class FilteredMaskedQuantile(Quantile): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
863 file_ext = 'filtered.masked.quan' |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
864 def __init__(self, **kwd): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
865 """Quantiles for chimera analysis""" |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
866 Quantile.__init__( self, **kwd ) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
867 self.masked = True |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
868 self.filtered = True |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
869 |
17
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
870 class LaneMask(Text): |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
871 file_ext = 'filter' |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
872 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
873 def sniff( self, filename ): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
874 """ |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
875 Determines whether the file is a lane mask filter: 1 line consisting of zeros and ones. |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
876 """ |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
877 try: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
878 fh = open( filename ) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
879 while True: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
880 buff = fh.read(1000) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
881 if not buff: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
882 break #EOF |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
883 else: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
884 if not re.match('^[01]+$',line): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
885 return False |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
886 return True |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
887 except: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
888 pass |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
889 finally: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
890 close(fh) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
891 return False |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
892 |
27
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
893 class CountTable(Tabular): |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
894 MetadataElement( name="groups", default=[], desc="Group Names", readonly=True, visible=True, no_value=[] ) |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
895 file_ext = 'count_table' |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
896 |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
897 def __init__(self, **kwd): |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
898 """ |
30
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
899 # http://www.mothur.org/wiki/Count_File |
27
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
900 A table with first column names and following columns integer counts |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
901 # Example 1: |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
902 Representative_Sequence total |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
903 U68630 1 |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
904 U68595 1 |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
905 U68600 1 |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
906 # Example 2 (with group columns): |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
907 Representative_Sequence total forest pasture |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
908 U68630 1 1 0 |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
909 U68595 1 1 0 |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
910 U68600 1 1 0 |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
911 U68591 1 1 0 |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
912 U68647 1 0 1 |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
913 """ |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
914 Tabular.__init__( self, **kwd ) |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
915 self.column_names = ['name','total'] |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
916 |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
917 def set_meta( self, dataset, overwrite = True, skip = 1, max_data_lines = None, **kwd ): |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
918 try: |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
919 data_lines = 0; |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
920 fh = open( dataset.file_name ) |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
921 line = fh.readline() |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
922 if line: |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
923 line = line.strip() |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
924 colnames = line.split() |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
925 if len(colnames) > 1: |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
926 dataset.metadata.columns = len( colnames ) |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
927 if len(colnames) > 2: |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
928 dataset.metadata.groups = colnames[2:] |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
929 column_types = ['str'] |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
930 for i in range(1,len(colnames)): |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
931 column_types.append('int') |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
932 dataset.metadata.column_types = column_types |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
933 dataset.metadata.comment_lines = 1 |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
934 while line: |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
935 line = fh.readline() |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
936 if not line: break |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
937 data_lines += 1 |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
938 dataset.metadata.data_lines = data_lines |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
939 finally: |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
940 close(fh) |
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
941 |
15
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
942 class RefTaxonomy(Tabular): |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
943 file_ext = 'ref.taxonomy' |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
944 """ |
30
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
945 # http://www.mothur.org/wiki/Taxonomy_outline |
15
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
946 A table with 2 or 3 columns: |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
947 - SequenceName |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
948 - Taxonomy (semicolon-separated taxonomy in descending order) |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
949 - integer ? |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
950 Example: 2-column ( http://www.mothur.org/wiki/Taxonomy_outline ) |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
951 X56533.1 Eukaryota;Alveolata;Ciliophora;Intramacronucleata;Oligohymenophorea;Hymenostomatida;Tetrahymenina;Glaucomidae;Glaucoma; |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
952 X97975.1 Eukaryota;Parabasalidea;Trichomonada;Trichomonadida;unclassified_Trichomonadida; |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
953 AF052717.1 Eukaryota;Parabasalidea; |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
954 Example: 3-column ( http://vamps.mbl.edu/resources/databases.php ) |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
955 v3_AA008 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus 5 |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
956 v3_AA016 Bacteria 120 |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
957 v3_AA019 Archaea;Crenarchaeota;Marine_Group_I 1 |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
958 """ |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
959 def __init__(self, **kwd): |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
960 Tabular.__init__( self, **kwd ) |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
961 self.column_names = ['name','taxonomy'] |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
962 |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
963 def sniff( self, filename ): |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
964 """ |
30
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
965 Determines whether the file is a Reference Taxonomy |
15
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
966 """ |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
967 try: |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
968 pat = '^([^ \t\n\r\x0c\x0b;]+([(]\\d+[)])?(;[^ \t\n\r\x0c\x0b;]+([(]\\d+[)])?)*(;)?)$' |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
969 fh = open( filename ) |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
970 count = 0 |
30
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
971 # VAMPS taxonomy files do not require a semicolon after the last taxonomy category |
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
972 # but assume assume the file will have some multi-level taxonomy assignments |
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
973 found_semicolons = False |
15
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
974 while True: |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
975 line = fh.readline() |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
976 if not line: |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
977 break #EOF |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
978 line = line.strip() |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
979 if line: |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
980 fields = line.split('\t') |
29
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
Jim Johnson <jj@umn.edu>
parents:
27
diff
changeset
|
981 if not (2 <= len(fields) <= 3): |
15
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
982 return False |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
983 if not re.match(pat,fields[1]): |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
984 return False |
30
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
985 if not found_semicolons and str(fields[1]).count(';') > 0: |
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
986 found_semicolons = True |
29
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
Jim Johnson <jj@umn.edu>
parents:
27
diff
changeset
|
987 if len(fields) == 3: |
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
Jim Johnson <jj@umn.edu>
parents:
27
diff
changeset
|
988 check = int(fields[2]) |
15
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
989 count += 1 |
30
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
990 if count > 100: |
15
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
991 break |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
992 if count > 0: |
30
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
993 # This will be true if at least one entry |
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
994 # has semicolons in the 2nd column |
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
995 return found_semicolons |
15
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
996 except: |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
997 pass |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
998 finally: |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
999 fh.close() |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1000 return False |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1001 |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1002 class SequenceTaxonomy(RefTaxonomy): |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1003 file_ext = 'seq.taxonomy' |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1004 """ |
30
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
1005 # http://www.mothur.org/wiki/Taxonomy_outline |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1006 A table with 2 columns: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1007 - SequenceName |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1008 - Taxonomy (semicolon-separated taxonomy in descending order) |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1009 Example: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1010 X56533.1 Eukaryota;Alveolata;Ciliophora;Intramacronucleata;Oligohymenophorea;Hymenostomatida;Tetrahymenina;Glaucomidae;Glaucoma; |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1011 X97975.1 Eukaryota;Parabasalidea;Trichomonada;Trichomonadida;unclassified_Trichomonadida; |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1012 AF052717.1 Eukaryota;Parabasalidea; |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1013 """ |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1014 def __init__(self, **kwd): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1015 Tabular.__init__( self, **kwd ) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1016 self.column_names = ['name','taxonomy'] |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1017 |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1018 def sniff( self, filename ): |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1019 """ |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1020 Determines whether the file is a SequenceTaxonomy |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1021 """ |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1022 try: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1023 pat = '^([^ \t\n\r\f\v;]+([(]\d+[)])?[;])+$' |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1024 fh = open( filename ) |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1025 count = 0 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1026 while True: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1027 line = fh.readline() |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1028 if not line: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1029 break #EOF |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1030 line = line.strip() |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1031 if line: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1032 fields = line.split('\t') |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1033 if len(fields) != 2: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1034 return False |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1035 if not re.match(pat,fields[1]): |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1036 return False |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1037 count += 1 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1038 if count > 10: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1039 break |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1040 if count > 0: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1041 return True |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1042 except: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1043 pass |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1044 finally: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1045 fh.close() |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1046 return False |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1047 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1048 class RDPSequenceTaxonomy(SequenceTaxonomy): |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1049 file_ext = 'rdp.taxonomy' |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1050 """ |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1051 A table with 2 columns: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1052 - SequenceName |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1053 - Taxonomy (semicolon-separated taxonomy in descending order, RDP requires exactly 6 levels deep) |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1054 Example: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1055 AB001518.1 Bacteria;Bacteroidetes;Sphingobacteria;Sphingobacteriales;unclassified_Sphingobacteriales; |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1056 AB001724.1 Bacteria;Cyanobacteria;Cyanobacteria;Family_II;GpIIa; |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1057 AB001774.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1058 """ |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1059 def sniff( self, filename ): |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1060 """ |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1061 Determines whether the file is a SequenceTaxonomy |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1062 """ |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1063 try: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1064 pat = '^([^ \t\n\r\f\v;]+([(]\d+[)])?[;]){6}$' |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1065 fh = open( filename ) |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1066 count = 0 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1067 while True: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1068 line = fh.readline() |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1069 if not line: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1070 break #EOF |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1071 line = line.strip() |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1072 if line: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1073 fields = line.split('\t') |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1074 if len(fields) != 2: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1075 return False |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1076 if not re.match(pat,fields[1]): |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1077 return False |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1078 count += 1 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1079 if count > 10: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1080 break |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1081 if count > 0: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1082 return True |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1083 except: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1084 pass |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1085 finally: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1086 fh.close() |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1087 return False |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1088 |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1089 class ConsensusTaxonomy(Tabular): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1090 file_ext = 'cons.taxonomy' |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1091 def __init__(self, **kwd): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1092 """A list of names""" |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1093 Tabular.__init__( self, **kwd ) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1094 self.column_names = ['OTU','count','taxonomy'] |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1095 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1096 class TaxonomySummary(Tabular): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1097 file_ext = 'tax.summary' |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1098 def __init__(self, **kwd): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1099 """A Summary of taxon classification""" |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1100 Tabular.__init__( self, **kwd ) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1101 self.column_names = ['taxlevel','rankID','taxon','daughterlevels','total'] |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1102 |
17
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1103 class Phylip(Text): |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1104 file_ext = 'phy' |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1105 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1106 def sniff( self, filename ): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1107 """ |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1108 Determines whether the file is in Phylip format (Interleaved or Sequential) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1109 The first line of the input file contains the number of species and the |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1110 number of characters, in free format, separated by blanks (not by |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1111 commas). The information for each species follows, starting with a |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1112 ten-character species name (which can include punctuation marks and blanks), |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1113 and continuing with the characters for that species. |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1114 http://evolution.genetics.washington.edu/phylip/doc/main.html#inputfiles |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1115 Interleaved Example: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1116 6 39 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1117 Archaeopt CGATGCTTAC CGCCGATGCT |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1118 HesperorniCGTTACTCGT TGTCGTTACT |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1119 BaluchitheTAATGTTAAT TGTTAATGTT |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1120 B. virginiTAATGTTCGT TGTTAATGTT |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1121 BrontosaurCAAAACCCAT CATCAAAACC |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1122 B.subtilisGGCAGCCAAT CACGGCAGCC |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1123 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1124 TACCGCCGAT GCTTACCGC |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1125 CGTTGTCGTT ACTCGTTGT |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1126 AATTGTTAAT GTTAATTGT |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1127 CGTTGTTAAT GTTCGTTGT |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1128 CATCATCAAA ACCCATCAT |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1129 AATCACGGCA GCCAATCAC |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1130 """ |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1131 try: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1132 fh = open( filename ) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1133 # counts line |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1134 line = fh.readline().strip() |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1135 linePieces = line.split() |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1136 count = int(linePieces[0]) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1137 seq_len = int(linePieces[1]) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1138 # data lines |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1139 """ |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1140 TODO check data lines |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1141 while True: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1142 line = fh.readline() |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1143 # name is the first 10 characters |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1144 name = line[0:10] |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1145 seq = line[10:].strip() |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1146 # nucleic base or amino acid 1-char designators (spaces allowed) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1147 bases = ''.join(seq.split()) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1148 # float per base (each separated by space) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1149 """ |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1150 return True |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1151 except: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1152 pass |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1153 finally: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1154 close(fh) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1155 return False |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1156 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1157 |
1
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1158 class Axes(Tabular): |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1159 file_ext = 'axes' |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1160 |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1161 def __init__(self, **kwd): |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1162 """Initialize axes datatype""" |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1163 Tabular.__init__( self, **kwd ) |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1164 def sniff( self, filename ): |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1165 """ |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1166 Determines whether the file is an axes format |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1167 The first line may have column headings. |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1168 The following lines have the name in the first column plus float columns for each axis. |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1169 ==> 98_sq_phylip_amazon.fn.unique.pca.axes <== |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1170 group axis1 axis2 |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1171 forest 0.000000 0.145743 |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1172 pasture 0.145743 0.000000 |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1173 |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1174 ==> 98_sq_phylip_amazon.nmds.axes <== |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1175 axis1 axis2 |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1176 U68589 0.262608 -0.077498 |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1177 U68590 0.027118 0.195197 |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1178 U68591 0.329854 0.014395 |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1179 """ |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1180 try: |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1181 fh = open( filename ) |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1182 count = 0 |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1183 line = fh.readline() |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1184 line = line.strip() |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1185 col_cnt = None |
30
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
1186 all_integers = True |
1
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1187 while True: |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1188 line = fh.readline() |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1189 line = line.strip() |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1190 if not line: |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1191 break #EOF |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1192 if line: |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1193 fields = line.split('\t') |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1194 if col_cnt == None: # ignore values in first line as they may be column headings |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1195 col_cnt = len(fields) |
29
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
Jim Johnson <jj@umn.edu>
parents:
27
diff
changeset
|
1196 # There should be at least 2 columns |
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
Jim Johnson <jj@umn.edu>
parents:
27
diff
changeset
|
1197 if col_cnt < 2: |
9c0cd3b92295
Fixes for metagenomics.py datatypes tahnks to Peter Briggs
Jim Johnson <jj@umn.edu>
parents:
27
diff
changeset
|
1198 return False |
1
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1199 else: |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1200 if len(fields) != col_cnt : |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1201 return False |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1202 try: |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1203 for i in range(1, col_cnt): |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1204 check = float(fields[i]) |
30
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
1205 # Also test for whether value is an integer |
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
1206 try: |
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
1207 check = int(fields[i]) |
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
1208 except ValueError: |
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
1209 all_integers = False |
1
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1210 except ValueError: |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1211 return False |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1212 count += 1 |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1213 if count > 10: |
30
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
1214 break |
1
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1215 if count > 0: |
30
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
1216 if not all_integers: |
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
1217 # At least one value was a float |
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
1218 return True |
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
1219 else: |
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
1220 return False |
1
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1221 except: |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1222 pass |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1223 finally: |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1224 fh.close() |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1225 return False |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
1226 |
15
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1227 class SffFlow(Tabular): |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1228 MetadataElement( name="flow_values", default="", no_value="", optional=True , desc="Total number of flow values", readonly=True) |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1229 MetadataElement( name="flow_order", default="TACG", no_value="TACG", desc="Total number of flow values", readonly=False) |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1230 file_ext = 'sff.flow' |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1231 """ |
30
a90d1915a176
metagenomics.py - require ref.taxonomy sniff to find at least 1 multi-level tax assignment with semicolon separators
Jim Johnson <jj@umn.edu>
parents:
29
diff
changeset
|
1232 # http://www.mothur.org/wiki/Flow_file |
15
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1233 The first line is the total number of flow values - 800 for Titanium data. For GS FLX it would be 400. |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1234 Following lines contain: |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1235 - SequenceName |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1236 - the number of useable flows as defined by 454's software |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1237 - the flow intensity for each base going in the order of TACG. |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1238 Example: |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1239 800 |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1240 GQY1XT001CQL4K 85 1.04 0.00 1.00 0.02 0.03 1.02 0.05 ... |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1241 GQY1XT001CQIRF 84 1.02 0.06 0.98 0.06 0.09 1.05 0.07 ... |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1242 GQY1XT001CF5YW 88 1.02 0.02 1.01 0.04 0.06 1.02 0.03 ... |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1243 """ |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1244 def __init__(self, **kwd): |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1245 Tabular.__init__( self, **kwd ) |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1246 |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1247 def set_meta( self, dataset, overwrite = True, skip = 1, max_data_lines = None, **kwd ): |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1248 Tabular.set_meta(self, dataset, overwrite, 1, max_data_lines) |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1249 try: |
16
541e3c97c240
Mothur - fix set_meta for SffFlow in datatypes/metagenomics.py
Jim Johnson <jj@umn.edu>
parents:
15
diff
changeset
|
1250 fh = open( dataset.file_name ) |
15
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1251 line = fh.readline() |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1252 line = line.strip() |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1253 flow_values = int(line) |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1254 dataset.metadata.flow_values = flow_values |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1255 finally: |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1256 fh.close() |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1257 |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1258 def make_html_table( self, dataset, skipchars=[] ): |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1259 """Create HTML table, used for displaying peek""" |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1260 out = ['<table cellspacing="0" cellpadding="3">'] |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1261 comments = [] |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1262 try: |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1263 # Generate column header |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1264 out.append('<tr>') |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1265 out.append( '<th>%d. Name</th>' % 1 ) |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1266 out.append( '<th>%d. Flows</th>' % 2 ) |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1267 for i in range( 3, dataset.metadata.columns+1 ): |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1268 base = dataset.metadata.flow_order[(i+1)%4] |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1269 out.append( '<th>%d. %d %s</th>' % (i-2,base) ) |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1270 out.append('</tr>') |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1271 out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) ) |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1272 out.append( '</table>' ) |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1273 out = "".join( out ) |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1274 except Exception, exc: |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1275 out = "Can't create peek %s" % str( exc ) |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1276 return out |
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1277 |
17
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1278 class Newick( Text ): |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1279 """ |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1280 The Newick Standard for representing trees in computer-readable form makes use of the correspondence between trees and nested parentheses. |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1281 http://evolution.genetics.washington.edu/phylip/newicktree.html |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1282 http://en.wikipedia.org/wiki/Newick_format |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1283 Example: |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1284 (B,(A,C,E),D); |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1285 or example with branch lengths: |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1286 (B:6.0,(A:5.0,C:3.0,E:4.0):5.0,D:11.0); |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1287 or an example with embedded comments but no branch lengths: |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1288 ((a [&&PRIME S=x], b [&&PRIME S=y]), c [&&PRIME S=z]); |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1289 Example with named interior noe: |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1290 (B:6.0,(A:5.0,C:3.0,E:4.0)Ancestor1:5.0,D:11.0); |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1291 """ |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1292 file_ext = 'tre' |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1293 |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1294 def __init__(self, **kwd): |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1295 Text.__init__( self, **kwd ) |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1296 |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1297 def sniff( self, filename ): ## TODO |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1298 """ |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1299 Determine whether the file is in Newick format |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1300 Note: Last non-space char of a tree should be a semicolon: ';' |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1301 Usually the first char will be a open parenthesis: '(' |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1302 (,,(,)); no nodes are named |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1303 (A,B,(C,D)); leaf nodes are named |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1304 (A,B,(C,D)E)F; all nodes are named |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1305 (:0.1,:0.2,(:0.3,:0.4):0.5); all but root node have a distance to parent |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1306 (:0.1,:0.2,(:0.3,:0.4):0.5):0.0; all have a distance to parent |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1307 (A:0.1,B:0.2,(C:0.3,D:0.4):0.5); distances and leaf names (popular) |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1308 (A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F; distances and all names |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1309 ((B:0.2,(C:0.3,D:0.4)E:0.5)F:0.1)A; a tree rooted on a leaf node (rare) |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1310 """ |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1311 if not os.path.exists(filename): |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1312 return False |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1313 try: |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1314 ## For now, guess this is a Newick file if it starts with a '(' and ends with a ';' |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1315 flen = os.path.getsize(filename) |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1316 fh = open( filename ) |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1317 len = min(flen,2000) |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1318 # check end of the file for a semicolon |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1319 fh.seek(-len,os.SEEK_END) |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1320 buf = fh.read(len).strip() |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1321 buf = buf.strip() |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1322 if not buf.endswith(';'): |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1323 return False |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1324 # See if this starts with a open parenthesis |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1325 if len < flen: |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1326 fh.seek(0) |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1327 buf = fh.read(len).strip() |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1328 if buf.startswith('('): |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1329 return True |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1330 except: |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1331 pass |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1332 finally: |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1333 close(fh) |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1334 return False |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1335 |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1336 class Nhx( Newick ): |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1337 """ |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1338 New Hampshire eXtended Newick with embedded |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1339 The Newick Standard for representing trees in computer-readable form makes use of the correspondence between trees and nested parentheses. |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1340 http://evolution.genetics.washington.edu/phylip/newicktree.html |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1341 http://en.wikipedia.org/wiki/Newick_format |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1342 Example: |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1343 (gene1_Hu[&&NHX:S=Hu_Homo_sapiens], (gene2_Hu[&&NHX:S=Hu_Homo_sapiens], gene2_Mu[&&NHX:S=Mu_Mus_musculus])); |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1344 """ |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1345 file_ext = 'nhx' |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1346 |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1347 class Nexus( Text ): |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1348 """ |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1349 http://en.wikipedia.org/wiki/Nexus_file |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1350 Example: |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1351 #NEXUS |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1352 BEGIN TAXA; |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1353 Dimensions NTax=4; |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1354 TaxLabels fish frog snake mouse; |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1355 END; |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1356 |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1357 BEGIN CHARACTERS; |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1358 Dimensions NChar=20; |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1359 Format DataType=DNA; |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1360 Matrix |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1361 fish ACATA GAGGG TACCT CTAAG |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1362 frog ACATA GAGGG TACCT CTAAG |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1363 snake ACATA GAGGG TACCT CTAAG |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1364 mouse ACATA GAGGG TACCT CTAAG |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1365 END; |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1366 |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1367 BEGIN TREES; |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1368 Tree best=(fish, (frog, (snake, mouse))); |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1369 END; |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1370 """ |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1371 file_ext = 'nex' |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1372 |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1373 def __init__(self, **kwd): |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1374 Text.__init__( self, **kwd ) |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1375 |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1376 def sniff( self, filename ): |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1377 """ |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1378 Determines whether the file is in nexus format |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1379 First line should be: |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1380 #NEXUS |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1381 """ |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1382 try: |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1383 fh = open( filename ) |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1384 count = 0 |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1385 line = fh.readline() |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1386 line = line.strip() |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1387 if line and line == '#NEXUS': |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1388 fh.close() |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1389 return True |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1390 except: |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1391 pass |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1392 finally: |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1393 fh.close() |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1394 return False |
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1395 |
15
a6189f58fedb
Mothur - updated for Mothur version 1.22.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1396 |
26
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1397 ## Biom |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1398 |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1399 class BiologicalObservationMatrix( Text ): |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1400 file_ext = 'biom' |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1401 """ |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1402 http://biom-format.org/documentation/biom_format.html |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1403 The format of the file is JSON: |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1404 { |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1405 "id":null, |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1406 "format": "Biological Observation Matrix 0.9.1-dev", |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1407 "format_url": "http://biom-format.org", |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1408 "type": "OTU table", |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1409 "generated_by": "QIIME revision 1.4.0-dev", |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1410 "date": "2011-12-19T19:00:00", |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1411 "rows":[ |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1412 {"id":"GG_OTU_1", "metadata":null}, |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1413 {"id":"GG_OTU_2", "metadata":null}, |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1414 {"id":"GG_OTU_3", "metadata":null}, |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1415 ], |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1416 "columns": [ |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1417 {"id":"Sample1", "metadata":null}, |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1418 {"id":"Sample2", "metadata":null} |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1419 ], |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1420 "matrix_type": "sparse", |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1421 "matrix_element_type": "int", |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1422 "shape": [3, 2], |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1423 "data":[[0,1,1], |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1424 [1,0,5], |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1425 [2,1,4] |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1426 ] |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1427 } |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1428 |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1429 """ |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1430 |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1431 def __init__(self, **kwd): |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1432 Text.__init__( self, **kwd ) |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1433 |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1434 def sniff( self, filename ): |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1435 if os.path.getsize(filename) < 50000: |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1436 try: |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1437 data = simplejson.load(open(filename)) |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1438 if data['format'].find('Biological Observation Matrix'): |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1439 return True |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1440 except: |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1441 pass |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1442 return False |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1443 |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1444 |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1445 |
5c77423823cb
Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
1446 |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1447 ## Qiime Classes |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1448 |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1449 class QiimeMetadataMapping(Tabular): |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1450 MetadataElement( name="column_names", default=[], desc="Column Names", readonly=False, visible=True, no_value=[] ) |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1451 file_ext = 'qiimemapping' |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1452 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1453 def __init__(self, **kwd): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1454 """ |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1455 http://qiime.sourceforge.net/documentation/file_formats.html#mapping-file-overview |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1456 Information about the samples necessary to perform the data analysis. |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1457 # self.column_names = ['#SampleID','BarcodeSequence','LinkerPrimerSequence','Description'] |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1458 """ |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1459 Tabular.__init__( self, **kwd ) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1460 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1461 def sniff( self, filename ): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1462 """ |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1463 Determines whether the file is a qiime mapping file |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1464 Just checking for an appropriate header line for now, could be improved |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1465 """ |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1466 try: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1467 pat = '#SampleID(\t[a-zA-Z][a-zA-Z0-9_]*)*\tDescription' |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1468 fh = open( filename ) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1469 while True: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1470 line = dataset_fh.readline() |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1471 if re.match(pat,line): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1472 return True |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1473 except: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1474 pass |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1475 finally: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1476 close(fh) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1477 return False |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1478 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1479 def set_column_names(self, dataset): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1480 if dataset.has_data(): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1481 dataset_fh = open( dataset.file_name ) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1482 line = dataset_fh.readline() |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1483 if line.startswith('#SampleID'): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1484 dataset.metadata.column_names = line.strip().split('\t'); |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1485 dataset_fh.close() |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1486 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1487 def set_meta( self, dataset, overwrite = True, skip = None, max_data_lines = None, **kwd ): |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1488 Tabular.set_meta(self, dataset, overwrite, skip, max_data_lines) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1489 self.set_column_names(dataset) |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1490 |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1491 class QiimeOTU(Tabular): |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1492 """ |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1493 Associates OTUs with sequence IDs |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1494 Example: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1495 0 FLP3FBN01C2MYD FLP3FBN01B2ALM |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1496 1 FLP3FBN01DF6NE FLP3FBN01CKW1J FLP3FBN01CHVM4 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1497 2 FLP3FBN01AXQ2Z |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1498 """ |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1499 file_ext = 'qiimeotu' |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1500 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1501 class QiimeOTUTable(Tabular): |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1502 """ |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1503 #Full OTU Counts |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1504 #OTU ID PC.354 PC.355 PC.356 Consensus Lineage |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1505 0 0 1 0 Root;Bacteria;Firmicutes;"Clostridia";Clostridiales |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1506 1 1 3 1 Root;Bacteria |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1507 2 0 2 2 Root;Bacteria;Bacteroidetes |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1508 """ |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1509 MetadataElement( name="column_names", default=[], desc="Column Names", readonly=False, visible=True, no_value=[] ) |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1510 file_ext = 'qiimeotutable' |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1511 def init_meta( self, dataset, copy_from=None ): |
27
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
1512 Tabular.init_meta( self, dataset, copy_from=copy_from ) |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1513 def set_meta( self, dataset, overwrite = True, skip = None, **kwd ): |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1514 self.set_column_names(dataset) |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1515 def set_column_names(self, dataset): |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1516 if dataset.has_data(): |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1517 dataset_fh = open( dataset.file_name ) |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1518 line = dataset_fh.readline() |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1519 line = dataset_fh.readline() |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1520 if line.startswith('#OTU ID'): |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1521 dataset.metadata.column_names = line.strip().split('\t'); |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1522 dataset_fh.close() |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1523 dataset.metadata.comment_lines = 2 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1524 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1525 class QiimeDistanceMatrix(Tabular): |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1526 """ |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1527 PC.354 PC.355 PC.356 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1528 PC.354 0.0 3.177 1.955 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1529 PC.355 3.177 0.0 3.444 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1530 PC.356 1.955 3.444 0.0 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1531 """ |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1532 file_ext = 'qiimedistmat' |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1533 def init_meta( self, dataset, copy_from=None ): |
27
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
26
diff
changeset
|
1534 Tabular.init_meta( self, dataset, copy_from=copy_from ) |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1535 def set_meta( self, dataset, overwrite = True, skip = None, **kwd ): |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1536 self.set_column_names(dataset) |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1537 def set_column_names(self, dataset): |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1538 if dataset.has_data(): |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1539 dataset_fh = open( dataset.file_name ) |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1540 line = dataset_fh.readline() |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1541 # first line contains the names |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1542 dataset.metadata.column_names = line.strip().split('\t'); |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1543 dataset_fh.close() |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1544 dataset.metadata.comment_lines = 1 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1545 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1546 class QiimePCA(Tabular): |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1547 """ |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1548 Principal Coordinate Analysis Data |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1549 The principal coordinate (PC) axes (columns) for each sample (rows). |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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parents:
1
diff
changeset
|
1550 Pairs of PCs can then be graphed to view the relationships between samples. |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1551 The bottom of the output file contains the eigenvalues and % variation explained for each PC. |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1552 Example: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1553 pc vector number 1 2 3 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1554 PC.354 -0.309063936588 0.0398252112257 0.0744672231759 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1555 PC.355 -0.106593922619 0.141125998277 0.0780204374172 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1556 PC.356 -0.219869362955 0.00917241121781 0.0357281314115 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1557 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1558 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1559 eigvals 0.480220500471 0.163567082874 0.125594470811 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1560 % variation explained 51.6955484555 17.6079322939 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1561 """ |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1562 file_ext = 'qiimepca' |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1563 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1564 class QiimeParams(Tabular): |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1565 """ |
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Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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1
diff
changeset
|
1566 ###pick_otus_through_otu_table.py parameters### |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
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1
diff
changeset
|
1567 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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1
diff
changeset
|
1568 # OTU picker parameters |
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Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
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1
diff
changeset
|
1569 pick_otus:otu_picking_method uclust |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1570 pick_otus:clustering_algorithm furthest |
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Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1571 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1572 # Representative set picker parameters |
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Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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1
diff
changeset
|
1573 pick_rep_set:rep_set_picking_method first |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1574 pick_rep_set:sort_by otu |
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Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1575 """ |
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Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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1
diff
changeset
|
1576 file_ext = 'qiimeparams' |
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Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1577 |
17
57df76d861e4
Modifications for ToolShed proprietary data types
Jim Johnson <jj@umn.edu>
parents:
16
diff
changeset
|
1578 class QiimePrefs(Text): |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1579 """ |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
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1
diff
changeset
|
1580 A text file, containing coloring preferences to be used by make_distance_histograms.py, make_2d_plots.py and make_3d_plots.py. |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1581 Example: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1582 { |
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Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1583 'background_color':'black', |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1584 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1585 'sample_coloring': |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1586 { |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1587 'Treatment': |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1588 { |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1589 'column':'Treatment', |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1590 'colors':(('red',(0,100,100)),('blue',(240,100,100))) |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1591 }, |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1592 'DOB': |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1593 { |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1594 'column':'DOB', |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1595 'colors':(('red',(0,100,100)),('blue',(240,100,100))) |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1596 } |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1597 }, |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1598 'MONTE_CARLO_GROUP_DISTANCES': |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1599 { |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1600 'Treatment': 10, |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1601 'DOB': 10 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1602 } |
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Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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1
diff
changeset
|
1603 } |
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Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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1
diff
changeset
|
1604 """ |
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Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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1
diff
changeset
|
1605 file_ext = 'qiimeprefs' |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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1
diff
changeset
|
1606 |
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Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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1
diff
changeset
|
1607 class QiimeTaxaSummary(Tabular): |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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1
diff
changeset
|
1608 """ |
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Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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1
diff
changeset
|
1609 Taxon PC.354 PC.355 PC.356 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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1
diff
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|
1610 Root;Bacteria;Actinobacteria 0.0 0.177 0.955 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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1
diff
changeset
|
1611 Root;Bacteria;Firmicutes 0.177 0.0 0.444 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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1
diff
changeset
|
1612 Root;Bacteria;Proteobacteria 0.955 0.444 0.0 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
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1
diff
changeset
|
1613 """ |
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1
diff
changeset
|
1614 MetadataElement( name="column_names", default=[], desc="Column Names", readonly=False, visible=True, no_value=[] ) |
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Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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1
diff
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|
1615 file_ext = 'qiimetaxsummary' |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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1
diff
changeset
|
1616 |
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1
diff
changeset
|
1617 def set_column_names(self, dataset): |
e990ac8a0f58
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1
diff
changeset
|
1618 if dataset.has_data(): |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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1
diff
changeset
|
1619 dataset_fh = open( dataset.file_name ) |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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1
diff
changeset
|
1620 line = dataset_fh.readline() |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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1
diff
changeset
|
1621 if line.startswith('Taxon'): |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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1
diff
changeset
|
1622 dataset.metadata.column_names = line.strip().split('\t'); |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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1
diff
changeset
|
1623 dataset_fh.close() |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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1
diff
changeset
|
1624 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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1
diff
changeset
|
1625 def set_meta( self, dataset, overwrite = True, skip = None, max_data_lines = None, **kwd ): |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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1
diff
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|
1626 Tabular.set_meta(self, dataset, overwrite, skip, max_data_lines) |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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1
diff
changeset
|
1627 self.set_column_names(dataset) |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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1
diff
changeset
|
1628 |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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parents:
diff
changeset
|
1629 if __name__ == '__main__': |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1630 import doctest, sys |
3202a38e44d9
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parents:
diff
changeset
|
1631 doctest.testmod(sys.modules[__name__]) |
3202a38e44d9
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diff
changeset
|
1632 |