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3 <title>MayaChemTools:Documentation:ExtractFromTextFiles.pl</title>
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13 <div class="DocNav">
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14 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./ExtractFromSequenceFiles.html" title="ExtractFromSequenceFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./FilterSDFiles.html" title="FilterSDFiles.html">Next</a></td><td width="34%" align="middle"><strong>ExtractFromTextFiles.pl</strong></td><td width="33%" align="right"><a href="././code/ExtractFromTextFiles.html" title="View source code">Code</a> | <a href="./../pdf/ExtractFromTextFiles.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/ExtractFromTextFiles.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/ExtractFromTextFiles.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/ExtractFromTextFiles.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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16 </table>
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17 </div>
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18 <p>
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19 </p>
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20 <h2>NAME</h2>
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21 <p>ExtractFromTextFiles.pl - Extract specific data from TextFile(s)</p>
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22 <p>
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23 </p>
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24 <h2>SYNOPSIS</h2>
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25 <p>ExtractFromTextFiles.pl TextFile(s)...</p>
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26 <p>ExtractFromTextFiles.pl [<strong>-c, --colmode</strong> colnum | collabel] [<strong>--categorycol </strong> number | string]
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27 [<strong>--columns</strong> "colnum,[colnum]..." | "collabel,[collabel]..."] [<strong>-h, --help</strong>]
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28 [<strong>--indelim</strong> <em>comma | semicolon</em>] [<strong>-m, --mode </strong> <em>columns | rows | categories</em>]
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29 [<strong>-o, --overwrite</strong>] [<strong>--outdelim</strong> <em>comma | tab | semicolon</em>] [<strong>-q, --quote</strong> <em>yes | no</em>]
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30 [<strong>--rows</strong> "colid,value,criteria..." | "colid,value..." | "colid,mincolvalue,maxcolvalue" | "rownum,rownum,..." | colid | "minrownum,maxrownum"]
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31 [ <strong>--rowsmode</strong> rowsbycolvalue | rowsbycolvaluelist | rowsbycolvaluerange | rowbymincolvalue | rowbymaxcolvalue | rownums | rownumrange]
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32 [<strong>-r, --root</strong> <em>rootname</em>] [<strong>-w, --workingdir</strong> <em>dirname</em>] TextFile(s)...</p>
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33 <p>
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34 </p>
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35 <h2>DESCRIPTION</h2>
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36 <p>Extract column(s)/row(s) data from <em>TextFile(s)</em> identified by column numbers or labels. Or categorize
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37 data using a specified column category. During categorization, a summary text file is
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38 generated containing category name and count; an additional text file, containing data for
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39 for each category, is also generated. The file names are separated by space. The
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40 valid file extensions are <em>.csv</em> and <em>.tsv</em> for comma/semicolon and tab delimited
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41 text files respectively. All other file names are ignored. All the text files in a
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42 current directory can be specified by <em>*.csv</em>, <em>*.tsv</em>, or the current directory
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43 name. The <strong>--indelim</strong> option determines the format of <em>TextFile(s)</em>. Any file
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44 which doesn't correspond to the format indicated by <strong>--indelim</strong> option is ignored.</p>
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45 <p>
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46 </p>
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47 <h2>OPTIONS</h2>
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48 <dl>
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49 <dt><strong><strong>-c, --colmode</strong> <em>colnum | collabel</em></strong></dt>
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50 <dd>
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51 <p>Specify how columns are identified in <em>TextFile(s)</em>: using column number or column
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52 label. Possible values: <em>colnum or collabel</em>. Default value: <em>colnum</em>.</p>
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53 </dd>
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54 <dt><strong><strong>--categorycol </strong> <em>number | string</em></strong></dt>
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55 <dd>
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56 <p>Column used to categorize data. Default value: First column.</p>
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57 <p>For <em>colnum</em> value of <strong>-c, --colmode</strong> option, input value is a column number.
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58 Example: <em>1</em>.</p>
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59 <p>For <em>collabel</em> value of <strong>-c, --colmode</strong> option, input value is a column label.
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60 Example: <em>Mol_ID</em>.</p>
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61 </dd>
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62 <dt><strong><strong>--columns</strong> <em>"colnum,[colnum]..." | "collabel,[collabel]..."</em></strong></dt>
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63 <dd>
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64 <p>List of comma delimited columns to extract. Default value: First column.</p>
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65 <p>For <em>colnum</em> value of <strong>-c, --colmode</strong> option, input values format is:
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66 <em>colnum,colnum,...</em>. Example: <em>1,3,5</em></p>
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67 <p>For <em>collabel</em> value of <strong>-c, --colmode</strong> option, input values format is:
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68 <em>collabel,collabel,..</em>. Example: <em>Mol_ID,MolWeight</em></p>
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69 </dd>
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70 <dt><strong><strong>-h, --help</strong></strong></dt>
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71 <dd>
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72 <p>Print this help message.</p>
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73 </dd>
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74 <dt><strong><strong>--indelim</strong> <em>comma | semicolon</em></strong></dt>
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75 <dd>
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76 <p>Input delimiter for CSV <em>TextFile(s)</em>. Possible values: <em>comma or semicolon</em>.
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77 Default value: <em>comma</em>. For TSV files, this option is ignored and <em>tab</em> is used as a
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78 delimiter.</p>
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79 </dd>
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80 <dt><strong><strong>-m, --mode </strong> <em>columns | rows | categories</em></strong></dt>
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81 <dd>
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82 <p>Specify what to extract from <em>TextFile(s)</em>. Possible values: <em>columns, rows,
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83 or categories</em>. Default value: <em>columns</em>.</p>
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84 <p>For <em>columns</em> mode, data for appropriate columns specified by <strong>--columns</strong> option
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85 is extracted from <em>TextFile(s)</em> and placed into new text files.</p>
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86 <p>For <em>rows</em> mode, appropriate rows specified in conjuction with <strong>--rowsmode</strong> and
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87 <strong>rows</strong> options are extracted from <em>TextFile(s)</em> and placed into new text files.</p>
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88 <p>For <em>categories</em> mode, coulmn specified by <strong>--categorycol</strong> is
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89 used to categorize data, and a summary text file is generated
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90 containing category name and count; an additional text file, containing data for
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91 for each category, is also generated.</p>
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92 </dd>
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93 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
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94 <dd>
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95 <p>Overwrite existing files.</p>
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96 </dd>
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97 <dt><strong><strong>--outdelim</strong> <em>comma | tab | semicolon</em>.</strong></dt>
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98 <dd>
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99 <p>Output text file delimiter. Possible values: <em>comma, tab, or semicolon</em>.
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100 Default value: <em>comma</em></p>
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101 </dd>
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102 <dt><strong><strong>-q, --quote</strong> <em>yes | no</em></strong></dt>
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103 <dd>
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104 <p>Put quotes around column values in output text file. Possible values: <em>yes or
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105 no</em>. Default value: <em>yes</em>.</p>
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106 </dd>
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107 <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt>
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108 <dd>
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109 <p>New file name is generated using the root: <Root>.<Ext>. Default for new file
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110 names: <TextFile>CategoriesSummary.<Ext>, <TextFile>ExtractedColumns.<Ext>, and
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111 <TextFile>ExtractedRows.<Ext> for <em>categories</em>, <em>columns</em>, and <em>rows</em> mode
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112 respectively. And <TextFile>Category<CategoryName>.<Ext>
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113 for each category retrieved from each text file. The output file type determines <Ext>
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114 value: csv and tsv for CSV, and TSV files respectively.</p>
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115 <p>This option is ignored for multiple input files.</p>
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116 </dd>
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117 <dt><strong><strong>--rows</strong> <em>"colid,value,criteria..." | "colid,value..." | "colid,mincolvalue,maxcolvalue" | "rownum,rownum,..." | colid | "minrownum,maxrownum"</em></strong></dt>
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118 <dd>
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119 <p>This value is <strong>--rowsmode</strong> specific. In general, it's a list of comma separated column ids and
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120 associated mode specific value. Based on Column ids specification, column label or number, is
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121 controlled by <strong>-c, --colmode</strong> option.</p>
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122 <p>First line containing column labels is always written out. And value comparisons assume
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123 numerical column data.</p>
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124 <p>For <em>rowsbycolvalue</em> mode, input value format contains these triplets:
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125 <em>colid,value, criteria...</em>. Possible values for criteria: <em>le, ge or eq</em>.
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126 Examples:</p>
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127 <div class="OptionsBox">
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128 MolWt,450,le
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129 <br/> MolWt,450,le,LogP,5,le,SumNumNO,10,le,SumNHOH,5,le</div>
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130 <p>For <em>rowsbycolvaluelist</em> mode, input value format is: <em>colid,value...</em>. Examples:</p>
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131 <div class="OptionsBox">
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132 Mol_ID,20
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133 <br/> Mol_ID,20,1002,1115</div>
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134 <p>For <em>rowsbycolvaluerange</em> mode, input value format is: <em>colid,mincolvalue,maxcolvalue</em>. Examples:</p>
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135 <div class="OptionsBox">
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136 MolWt,100,450</div>
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137 <p>For <em>rowbymincolvalue, rowbymaxcolvalue</em> modes, input value format is: <em>colid</em>.</p>
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138 <p>For <em>rownum</em> mode, input value format is: <em>rownum</em>. Default value: <em>2</em>.</p>
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139 <p>For <em>rownumrange</em> mode, input value format is: <em>minrownum, maxrownum</em>. Examples:</p>
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140 <div class="OptionsBox">
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141 10,40</div>
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142 </dd>
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143 <dt><strong><strong>--rowsmode</strong> <em>rowsbycolvalue | rowsbycolvaluelist | rowsbycolvaluerange | rowbymincolvalue | rowbymaxcolvalue | rownums | rownumrange</em></strong></dt>
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144 <dd>
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145 <p>Specify how to extract rows from <em>TextFile(s)</em>. Possible values: <em>rowsbycolvalue, rowsbycolvaluelist, rowsbycolvaluerange,
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146 rowbymincolvalue, rowbymaxcolvalue, rownum, rownumrange</em>. Default value: <em>rownum</em>.</p>
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147 <p>Use <strong>--rows</strong> option to list rows criterion used for extraction of rows from
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148 <em>TextFile(s)</em>.</p>
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149 </dd>
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150 <dt><strong><strong>-w, --workingdir</strong> <em>dirname</em></strong></dt>
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151 <dd>
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152 <p>Location of working directory. Default: current directory.</p>
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153 </dd>
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154 </dl>
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155 <p>
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156 </p>
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157 <h2>EXAMPLES</h2>
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158 <p>To extract first column from a text file and generate a new CSV text file NewSample1.csv,
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159 type:</p>
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160 <div class="ExampleBox">
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161 % ExtractFromTextFiles.pl -r NewSample1 -o Sample1.csv</div>
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162 <p>To extract columns Mol_ID, MolWeight, and NAME from Sample1.csv and generate a new
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163 textfile NewSample1.tsv with no quotes, type:</p>
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164 <div class="ExampleBox">
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165 % ExtractFromTextFiles.pl -m columns -c collabel --columns "Mol_ID,
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166 MolWeight,NAME" --outdelim tab --quote no -r NewSample1
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167 -o Sample1.csv</div>
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168 <p>To extract rows containing values for MolWeight column of less than 450 from
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169 Sample1.csv and generate a new textfile NewSample1.csv, type:</p>
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170 <div class="ExampleBox">
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171 % ExtractFromTextFiles.pl -m rows --rowsmode rowsbycolvalue
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172 -c collabel --rows MolWeight,450,le -r NewSample1
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173 -o Sample1.csv</div>
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174 <p>To extract rows containing values for MolWeight column between 400 and 500 from
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175 Sample1.csv and generate a new textfile NewSample1.csv, type:</p>
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176 <div class="ExampleBox">
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177 % ExtractFromTextFiles.pl -m rows --rowsmode rowsbycolvaluerange
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178 -c collabel --rows MolWeight,450,500 -r NewSample1
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179 -o Sample1.csv</div>
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180 <p>To extract a row containing minimum value for column MolWeight from Sample1.csv and generate
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181 a new textfile NewSample1.csv, type:</p>
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182 <div class="ExampleBox">
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183 % ExtractFromTextFiles.pl -m rows --rowsmode rowbymincolvalue
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184 -c collabel --rows MolWeight -r NewSample1
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185 -o Sample1.csv</div>
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186 <p>
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187 </p>
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188 <h2>AUTHOR</h2>
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189 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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190 <p>
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191 </p>
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192 <h2>SEE ALSO</h2>
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193 <p><a href="./JoinTextFiles.html">JoinTextFiles.pl</a>, <a href="./MergeTextFilesWithSD.html">MergeTextFilesWithSD.pl</a>, <a href="./ModifyTextFilesFormat.html">ModifyTextFilesFormat.pl</a>, <a href="./SplitTextFiles.html">SplitTextFiles.pl</a>
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194 </p>
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195 <p>
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196 </p>
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197 <h2>COPYRIGHT</h2>
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198 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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199 <p>This file is part of MayaChemTools.</p>
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200 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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201 the terms of the GNU Lesser General Public License as published by the Free
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202 Software Foundation; either version 3 of the License, or (at your option)
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203 any later version.</p>
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204 <p> </p><p> </p><div class="DocNav">
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205 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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206 <tr align="left" valign="top"><td width="33%" align="left"><a href="./ExtractFromSequenceFiles.html" title="ExtractFromSequenceFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./FilterSDFiles.html" title="FilterSDFiles.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>ExtractFromTextFiles.pl</strong></td></tr>
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207 </table>
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208 </div>
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209 <br />
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210 <center>
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211 <img src="../../images/h2o2.png">
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212 </center>
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