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1 NAME
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2 ExtractFromTextFiles.pl - Extract specific data from TextFile(s)
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3
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4 SYNOPSIS
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5 ExtractFromTextFiles.pl TextFile(s)...
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6
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7 ExtractFromTextFiles.pl [-c, --colmode colnum | collabel] [--categorycol
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8 number | string] [--columns "colnum,[colnum]..." |
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9 "collabel,[collabel]..."] [-h, --help] [--indelim *comma | semicolon*]
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10 [-m, --mode *columns | rows | categories*] [-o, --overwrite] [--outdelim
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11 *comma | tab | semicolon*] [-q, --quote *yes | no*] [--rows
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12 "colid,value,criteria..." | "colid,value..." |
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13 "colid,mincolvalue,maxcolvalue" | "rownum,rownum,..." | colid |
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14 "minrownum,maxrownum"] [ --rowsmode rowsbycolvalue | rowsbycolvaluelist
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15 | rowsbycolvaluerange | rowbymincolvalue | rowbymaxcolvalue | rownums |
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16 rownumrange] [-r, --root *rootname*] [-w, --workingdir *dirname*]
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17 TextFile(s)...
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18
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19 DESCRIPTION
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20 Extract column(s)/row(s) data from *TextFile(s)* identified by column
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21 numbers or labels. Or categorize data using a specified column category.
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22 During categorization, a summary text file is generated containing
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23 category name and count; an additional text file, containing data for
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24 for each category, is also generated. The file names are separated by
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25 space. The valid file extensions are *.csv* and *.tsv* for
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26 comma/semicolon and tab delimited text files respectively. All other
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27 file names are ignored. All the text files in a current directory can be
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28 specified by **.csv*, **.tsv*, or the current directory name. The
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29 --indelim option determines the format of *TextFile(s)*. Any file which
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30 doesn't correspond to the format indicated by --indelim option is
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31 ignored.
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32
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33 OPTIONS
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34 -c, --colmode *colnum | collabel*
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35 Specify how columns are identified in *TextFile(s)*: using column
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36 number or column label. Possible values: *colnum or collabel*.
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37 Default value: *colnum*.
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38
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39 --categorycol *number | string*
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40 Column used to categorize data. Default value: First column.
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41
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42 For *colnum* value of -c, --colmode option, input value is a column
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43 number. Example: *1*.
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44
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45 For *collabel* value of -c, --colmode option, input value is a
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46 column label. Example: *Mol_ID*.
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47
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48 --columns *"colnum,[colnum]..." | "collabel,[collabel]..."*
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49 List of comma delimited columns to extract. Default value: First
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50 column.
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51
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52 For *colnum* value of -c, --colmode option, input values format is:
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53 *colnum,colnum,...*. Example: *1,3,5*
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54
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55 For *collabel* value of -c, --colmode option, input values format
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56 is: *collabel,collabel,..*. Example: *Mol_ID,MolWeight*
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57
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58 -h, --help
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59 Print this help message.
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60
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61 --indelim *comma | semicolon*
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62 Input delimiter for CSV *TextFile(s)*. Possible values: *comma or
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63 semicolon*. Default value: *comma*. For TSV files, this option is
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64 ignored and *tab* is used as a delimiter.
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65
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66 -m, --mode *columns | rows | categories*
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67 Specify what to extract from *TextFile(s)*. Possible values:
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68 *columns, rows, or categories*. Default value: *columns*.
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69
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70 For *columns* mode, data for appropriate columns specified by
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71 --columns option is extracted from *TextFile(s)* and placed into new
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72 text files.
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73
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74 For *rows* mode, appropriate rows specified in conjuction with
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75 --rowsmode and rows options are extracted from *TextFile(s)* and
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76 placed into new text files.
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77
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78 For *categories* mode, coulmn specified by --categorycol is used to
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79 categorize data, and a summary text file is generated containing
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80 category name and count; an additional text file, containing data
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81 for for each category, is also generated.
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82
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83 -o, --overwrite
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84 Overwrite existing files.
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85
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86 --outdelim *comma | tab | semicolon*.
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87 Output text file delimiter. Possible values: *comma, tab, or
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88 semicolon*. Default value: *comma*
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89
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90 -q, --quote *yes | no*
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91 Put quotes around column values in output text file. Possible
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92 values: *yes or no*. Default value: *yes*.
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93
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94 -r, --root *rootname*
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95 New file name is generated using the root: <Root>.<Ext>. Default for
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96 new file names: <TextFile>CategoriesSummary.<Ext>,
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97 <TextFile>ExtractedColumns.<Ext>, and <TextFile>ExtractedRows.<Ext>
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98 for *categories*, *columns*, and *rows* mode respectively. And
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99 <TextFile>Category<CategoryName>.<Ext> for each category retrieved
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100 from each text file. The output file type determines <Ext> value:
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101 csv and tsv for CSV, and TSV files respectively.
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102
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103 This option is ignored for multiple input files.
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104
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105 --rows *"colid,value,criteria..." | "colid,value..." |
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106 "colid,mincolvalue,maxcolvalue" | "rownum,rownum,..." | colid |
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107 "minrownum,maxrownum"*
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108 This value is --rowsmode specific. In general, it's a list of comma
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109 separated column ids and associated mode specific value. Based on
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110 Column ids specification, column label or number, is controlled by
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111 -c, --colmode option.
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112
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113 First line containing column labels is always written out. And value
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114 comparisons assume numerical column data.
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115
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116 For *rowsbycolvalue* mode, input value format contains these
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117 triplets: *colid,value, criteria...*. Possible values for criteria:
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118 *le, ge or eq*. Examples:
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119
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120 MolWt,450,le
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121 MolWt,450,le,LogP,5,le,SumNumNO,10,le,SumNHOH,5,le
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122
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123 For *rowsbycolvaluelist* mode, input value format is:
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124 *colid,value...*. Examples:
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125
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126 Mol_ID,20
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127 Mol_ID,20,1002,1115
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128
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129 For *rowsbycolvaluerange* mode, input value format is:
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130 *colid,mincolvalue,maxcolvalue*. Examples:
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131
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132 MolWt,100,450
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133
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134 For *rowbymincolvalue, rowbymaxcolvalue* modes, input value format
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135 is: *colid*.
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136
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137 For *rownum* mode, input value format is: *rownum*. Default value:
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138 *2*.
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139
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140 For *rownumrange* mode, input value format is: *minrownum,
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141 maxrownum*. Examples:
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142
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143 10,40
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144
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145 --rowsmode *rowsbycolvalue | rowsbycolvaluelist | rowsbycolvaluerange |
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146 rowbymincolvalue | rowbymaxcolvalue | rownums | rownumrange*
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147 Specify how to extract rows from *TextFile(s)*. Possible values:
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148 *rowsbycolvalue, rowsbycolvaluelist, rowsbycolvaluerange,
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149 rowbymincolvalue, rowbymaxcolvalue, rownum, rownumrange*. Default
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150 value: *rownum*.
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151
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152 Use --rows option to list rows criterion used for extraction of rows
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153 from *TextFile(s)*.
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154
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155 -w, --workingdir *dirname*
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156 Location of working directory. Default: current directory.
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157
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158 EXAMPLES
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159 To extract first column from a text file and generate a new CSV text
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160 file NewSample1.csv, type:
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161
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162 % ExtractFromTextFiles.pl -r NewSample1 -o Sample1.csv
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163
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164 To extract columns Mol_ID, MolWeight, and NAME from Sample1.csv and
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165 generate a new textfile NewSample1.tsv with no quotes, type:
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166
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167 % ExtractFromTextFiles.pl -m columns -c collabel --columns "Mol_ID,
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168 MolWeight,NAME" --outdelim tab --quote no -r NewSample1
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169 -o Sample1.csv
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170
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171 To extract rows containing values for MolWeight column of less than 450
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172 from Sample1.csv and generate a new textfile NewSample1.csv, type:
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173
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174 % ExtractFromTextFiles.pl -m rows --rowsmode rowsbycolvalue
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175 -c collabel --rows MolWeight,450,le -r NewSample1
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176 -o Sample1.csv
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177
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178 To extract rows containing values for MolWeight column between 400 and
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179 500 from Sample1.csv and generate a new textfile NewSample1.csv, type:
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180
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181 % ExtractFromTextFiles.pl -m rows --rowsmode rowsbycolvaluerange
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182 -c collabel --rows MolWeight,450,500 -r NewSample1
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183 -o Sample1.csv
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184
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185 To extract a row containing minimum value for column MolWeight from
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186 Sample1.csv and generate a new textfile NewSample1.csv, type:
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187
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188 % ExtractFromTextFiles.pl -m rows --rowsmode rowbymincolvalue
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189 -c collabel --rows MolWeight -r NewSample1
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190 -o Sample1.csv
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191
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192 AUTHOR
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193 Manish Sud <msud@san.rr.com>
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194
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195 SEE ALSO
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196 JoinTextFiles.pl, MergeTextFilesWithSD.pl, ModifyTextFilesFormat.pl,
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197 SplitTextFiles.pl
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198
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199 COPYRIGHT
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200 Copyright (C) 2015 Manish Sud. All rights reserved.
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201
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202 This file is part of MayaChemTools.
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203
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204 MayaChemTools is free software; you can redistribute it and/or modify it
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205 under the terms of the GNU Lesser General Public License as published by
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206 the Free Software Foundation; either version 3 of the License, or (at
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207 your option) any later version.
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208
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