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1 NAME
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2 ExtractFromSDFiles.pl - Extract specific data from SDFile(s)
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3
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4 SYNOPSIS
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5 ExtractFromSDFiles.pl SDFile(s)...
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6
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7 ExtractFromSDFiles.pl [-h, --help] [-d, --datafields "fieldlabel,..." |
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8 "fieldlabel,value,criteria..." | "fieldlabel,value,value..."]
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9 [--datafieldsfile filename] [--indelim comma | tab | semicolon] [-m,
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10 --mode alldatafields | commondatafields | | datafieldnotbylist |
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11 datafields | datafieldsbyvalue | datafieldsbyregex | datafieldbylist |
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12 datafielduniquebylist | molnames | randomcmpds | recordnum | recordnums
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13 | recordrange | 2dcmpdrecords | 3dcmpdrecords ] [-n, --numofcmpds
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14 number] [--outdelim comma | tab | semicolon] [--output SD | text | both]
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15 [-o, --overwrite] [-q, --quote yes | no] [--record recnum |
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16 startrecnum,endrecnum] --RegexIgnoreCase *yes or no* [-r, --root
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17 rootname] [-s, --seed number] [--StrDataString yes | no]
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18 [--StrDataStringDelimiter text] [--StrDataStringMode StrOnly |
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19 StrAndDataFields] [--ValueComparisonMode *Numeric | Alphanumeric*] [-v,
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20 --violations- number] [-w, --workingdir dirname] SDFile(s)...
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21
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22 DESCRIPTION
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23 Extract specific data from *SDFile(s)* and generate appropriate SD or
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24 CSV/TSV text file(s). The structure data from SDFile(s) is not
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25 transferred to CSV/TSV text file(s). Multiple SDFile names are separated
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26 by spaces. The valid file extensions are *.sdf* and *.sd*. All other
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27 file names are ignored. All the SD files in a current directory can be
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28 specified either by **.sdf* or the current directory name.
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29
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30 OPTIONS
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31 -h, --help
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32 Print this help message.
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33
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34 -d, --datafields *"fieldlabel,..." | "fieldlabel,value,criteria..." |
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35 "fieldlabel,value,value,..."*
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36 This value is mode specific. In general, it's a list of comma
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37 separated data field labels and associated mode specific values.
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38
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39 For *datafields* mode, input value format is: *fieldlabel,...*.
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40 Examples:
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41
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42 Extreg
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43 Extreg,CompoundName,ID
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44
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45 For *datafieldsbyvalue* mode, input value format contains these
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46 triplets: *fieldlabel,value, criteria...*. Possible values for
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47 criteria: *le, ge or eq*. The values of --ValueComparisonMode
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48 indicates whether values are compared numerical or string comarison
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49 operators. Default is to consider data field values as numerical
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50 values and use numerical comparison operators. Examples:
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51
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52 MolWt,450,le
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53 MolWt,450,le,LogP,5,le,SumNumNO,10,le,SumNHOH,5,le
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54
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55 For *datafieldsbyregex* mode, input value format contains these
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56 triplets: *fieldlabel,regex, criteria...*. *regex* corresponds to
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57 any valid regular expression and is used to match the values for
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58 specified *fieldlabel*. Possible values for criteria: *eq or ne*.
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59 During *eq* and *ne* values, data field label value is matched with
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60 regular expression using =~ and !~ respectively. --RegexIgnoreCase
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61 option value is used to determine whether to ignore letter
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62 upper/lower case during regular expression match. Examples:
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63
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64 Name,ol,eq
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65 Name,'^pat',ne
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66
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67 For *datafieldbylist* and *datafielduniquebylist* mode, input value
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68 format is: *fieldlabel,value1,value2...*. This is equivalent to
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69 *datafieldsbyvalue* mode with this input value
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70 format:*fieldlabel,value1,eq,fieldlabel,value2,eq,...*. For
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71 *datafielduniquebylist* mode, only unique compounds identified by
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72 first occurrence of *value* associated with *fieldlabel* in
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73 *SDFile(s)* are kept; any subsequent compounds are simply ignored.
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74
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75 For *datafieldnotbylist* mode, input value format is:
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76 *fieldlabel,value1,value2...*. In this mode, the script behaves
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77 exactly opposite of *datafieldbylist* mode, and only those compounds
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78 are extracted whose data field values don't match any specified data
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79 field value.
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80
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81 --datafieldsfile *filename*
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82 Filename which contains various mode specific values. This option
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83 provides a way to specify mode specific values in a file instead of
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84 entering them on the command line using -d --datafields.
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85
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86 For *datafields* mode, input file lines contain comma delimited
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87 field labels: *fieldlabel,...*. Example:
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88
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89 Line 1:MolId
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90 Line 2:"Extreg",CompoundName,ID
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91
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92 For *datafieldsbyvalue* mode, input file lines contains these comma
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93 separated triplets: *fieldlabel,value, criteria*. Possible values
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94 for criteria: *le, ge or eq*. Examples:
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95
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96 Line 1:MolWt,450,le
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97
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98 Line 1:"MolWt",450,le,"LogP",5,le,"SumNumNO",10,le,"SumNHOH",5,le
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99
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100 Line 1:MolWt,450,le
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101 Line 2:"LogP",5,le
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102 Line 3:"SumNumNO",10,le
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103 Line 4: SumNHOH,5,le
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104
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105 For *datafieldbylist* and *datafielduniquebylist* mode, input file
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106 line format is:
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107
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108 Line 1:fieldlabel;
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109 Subsequent lines:value1,value2...
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110
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111 For *datafieldbylist*, *datafielduniquebylist*, and
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112 *datafieldnotbylist* mode, input file line format is:
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113
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114 Line 1:fieldlabel;
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115 Subsequent lines:value1,value2...
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116
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117 For *datafielduniquebylist* mode, only unique compounds identified
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118 by first occurrence of *value* associated with *fieldlabel* in
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119 *SDFile(s)* are kept; any subsequent compounds are simply ignored.
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120 Example:
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121
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122 Line 1: MolID
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123 Subsequent Lines:
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124 907508
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125 832291,4642
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126 "1254","907303"
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127
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128 --indelim *comma | tab | semicolon*
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129 Delimiter used to specify text values for -d --datafields and
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130 --datafieldsfile options. Possible values: *comma, tab, or
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131 semicolon*. Default value: *comma*.
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132
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133 -m, --mode *alldatafields | commondatafields | datafields |
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134 datafieldsbyvalue | datafieldsbyregex | datafieldbylist |
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135 datafielduniquebylist | datafieldnotbylist | molnames | randomcmpds |
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136 recordnum | recordnums | recordrange | 2dcmpdrecords | 3dcmpdrecords*
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137 Specify what to extract from *SDFile(s)*. Possible values:
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138 *alldatafields, commondatafields, datafields, datafieldsbyvalue,
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139 datafieldsbyregex, datafieldbylist, datafielduniquebylist,
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140 datafieldnotbylist, molnames, randomcmpds, recordnum, recordnums,
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141 recordrange, 2dcmpdrecords, 3dcmpdrecords*. Default value:
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142 *alldatafields*.
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143
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144 For *alldatafields* and *molnames* mode, only a CSV/TSV text file is
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145 generated; for all other modes, however, a SD file is generated by
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146 default - you can change the behavior to genereate text file using
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147 *--output* option.
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148
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149 For *3DCmpdRecords* mode, only those compounds with at least one
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150 non-zero value for Z atomic coordinates are retrieved; however,
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151 during retrieval of compounds in *2DCmpdRecords* mode, all Z atomic
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152 coordinates must be zero.
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153
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154 -n, --numofcmpds *number*
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155 Number of compouds to extract during *randomcmpds* mode.
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156
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157 --outdelim *comma | tab | semicolon*
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158 Delimiter for output CSV/TSV text file(s). Possible values: *comma,
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159 tab, or semicolon* Default value: *comma*
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160
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161 --output *SD | text | both*
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162 Type of output files to generate. Possible values: *SD, text, or
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163 both*. Default value: *SD*. For *alldatafields* and *molnames* mode,
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164 this option is ingored and only a CSV/TSV text file is generated.
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165
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166 -o, --overwrite
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167 Overwrite existing files.
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168
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169 -q, --quote *yes | no*
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170 Put quote around column values in output CSV/TSV text file(s).
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171 Possible values: *yes or no*. Default value: *yes*.
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172
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173 --record *recnum | recnums | startrecnum,endrecnum*
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174 Record number, record numbers or range of records to extract during
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175 *recordnum*, *recordnums* and *recordrange* mode. Input value format
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176 is: <num>, <num1,num2,...> and <startnum, endnum> for *recordnum*,
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177 *recordnums* and *recordrange* modes recpectively. Default value:
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178 none.
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179
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180 --RegexIgnoreCase *yes or no*
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181 Specify whether to ingnore case during *datafieldsbyregex* value of
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182 -m, --mode option. Possible values: *yes or no*. Default value:
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183 *yes*.
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184
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185 -r, --root *rootname*
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186 New file name is generated using the root: <Root>.<Ext>. Default for
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187 new file names: <SDFileName><mode>.<Ext>. The file type determines
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188 <Ext> value. The sdf, csv, and tsv <Ext> values are used for SD,
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189 comma/semicolon, and tab delimited text files respectively.This
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190 option is ignored for multiple input files.
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191
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192 -s, --seed *number*
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193 Random number seed used for *randomcmpds* mode. Default:123456789.
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194
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195 --StrDataString *yes | no*
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196 Specify whether to write out structure data string to CSV/TSV text
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197 file(s). Possible values: *yes or no*. Default value: *no*.
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198
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199 The value of StrDataStringDelimiter option is used as a delimiter to
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200 join structure data lines into a structure data string.
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201
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202 This option is ignored during generation of SD file(s).
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203
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204 --StrDataStringDelimiter *text*
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205 Delimiter for joining multiple stucture data lines into a string
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206 before writing to CSV/TSV text file(s). Possible values: *any
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207 alphanumeric text*. Default value: *|*.
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208
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209 This option is ignored during generation of SD file(s).
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210
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211 --StrDataStringMode *StrOnly | StrAndDataFields*
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212 Specify whether to include SD data fields and values along with the
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213 structure data into structure data string before writing it out to
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214 CSV/TSV text file(s). Possible values: *StrOnly or
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215 StrAndDataFields*. Default value: *StrOnly*.
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216
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217 The value of StrDataStringDelimiter option is used as a delimiter to
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218 join structure data lines into a structure data string.
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219
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220 This option is ignored during generation of SD file(s).
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221
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222 --ValueComparisonMode *Numeric | Alphanumeric*
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223 Specify how to compare data field values during *datafieldsbyvalue*
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224 mode: Compare values using either numeric or string ((eq, le, ge)
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225 comparison operators. Possible values: *Numeric or Alphanumeric*.
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226 Defaule value: *Numeric*.
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227
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228 -v, --violations *number*
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229 Number of criterion violations allowed for values specified during
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230 *datafieldsbyvalue* and *datafieldsbyregex* mode. Default value:
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231 *0*.
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232
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233 -w, --workingdir *dirname*
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234 Location of working directory. Default: current directory.
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235
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236 EXAMPLES
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237 To retrieve all data fields from SD files and generate CSV text files,
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238 type:
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239
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240 % ExtractFromSDFiles.pl -o Sample.sdf
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241 % ExtractFromSDFiles.pl -o *.sdf
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242
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243 To retrieve all data fields from SD file and generate CSV text files
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244 containing a column with structure data as a string with | as line
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245 delimiter, type:
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246
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247 % ExtractFromSDFiles.pl --StrDataString Yes -o Sample.sdf
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248
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249 To retrieve MOL_ID data fileld from SD file and generate CSV text files
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250 containing a column with structure data along with all data fields as a
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251 string with | as line delimiter, type:
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252
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253 % ExtractFromSDFiles.pl -m datafields -d "Mol_ID" --StrDataString Yes
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254 --StrDataStringMode StrAndDataFields --StrDataStringDelimiter "|"
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255 --output text -o Sample.sdf
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256
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257 To retrieve common data fields which exists for all the compounds in a
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258 SD file and generate a TSV text file NewSample.tsv, type:
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259
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260 % ExtractFromSDFiles.pl -m commondatafields --outdelim tab -r NewSample
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261 --output Text -o Sample.sdf
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262
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263 To retrieve MolId, ExtReg, and CompoundName data field from a SD file
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264 and generate a CSV text file NewSample.csv, type:
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265
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266 % ExtractFromSDFiles.pl -m datafields -d "Mol_ID,MolWeight,
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267 CompoundName" -r NewSample --output Text -o Sample.sdf
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268
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269 To retrieve compounds from a SD which meet a specific set of criteria -
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270 MolWt <= 450, LogP <= 5 and SumNO < 10 - from a SD file and generate a
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271 new SD file NewSample.sdf, type:
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272
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273 % ExtractFromSDFiles.pl -m datafieldsbyvalue -d "MolWt,450,le,LogP
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274 ,5,le,SumNO,10" -r NewSample -o Sample.sdf
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275
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276 To retrive compounds from a SD file with a specific set of values for
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277 MolID and generate a new SD file NewSample.sdf, type:
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278
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279 % ExtractFromSDFiles.pl -m datafieldbylist -d "Mol_ID,159,4509,4619"
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280 -r NewSample -o Sample.sdf
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281
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282 To retrive compounds from a SD file with values for MolID not on a list
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283 of specified values and generate a new SD file NewSample.sdf, type:
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284
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285 % ExtractFromSDFiles.pl -m datafieldnotbylist -d "Mol_ID,159,4509,4619"
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286 -r NewSample -o Sample.sdf
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287
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288 To retrive 10 random compounds from a SD file and generate a new SD file
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289 RandomSample.sdf, type:
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290
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291 % ExtractFromSDFiles.pl -m randomcmpds -n 10 -r RandomSample
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292 -o Sample.sdf
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293
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294 To retrive compound record number 10 from a SD file and generate a new
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295 SD file NewSample.sdf, type:
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296
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297 % ExtractFromSDFiles.pl -m recordnum --record 10 -r NewSample
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298 -o Sample.sdf
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299
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300 To retrive compound record numbers 10, 20 and 30 from a SD file and
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301 generate a new SD file NewSample.sdf, type:
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302
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303 % ExtractFromSDFiles.pl -m recordnums --record 10,20,30 -r NewSample
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304 -o Sample.sdf
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305
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306 To retrive compound records between 10 to 20 from SD file and generate a
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307 new SD file NewSample.sdf, type:
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308
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309 % ExtractFromSDFiles.pl -m recordrange --record 10,20 -r NewSample
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310 -o Sample.sdf
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311
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312 AUTHOR
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313 Manish Sud <msud@san.rr.com>
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314
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315 SEE ALSO
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316 FilterSDFiles.pl, InfoSDFiles.pl, SplitSDFiles.pl,
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317 MergeTextFilesWithSD.pl
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318
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319 COPYRIGHT
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320 Copyright (C) 2015 Manish Sud. All rights reserved.
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321
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322 This file is part of MayaChemTools.
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323
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324 MayaChemTools is free software; you can redistribute it and/or modify it
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325 under the terms of the GNU Lesser General Public License as published by
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326 the Free Software Foundation; either version 3 of the License, or (at
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327 your option) any later version.
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328
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