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POawk - how to extract a pattern
 

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    <p>Asking for instructions about using awk to extract text blocks with specific rows from a file.</p> <p>The file has the following structure:</p> <pre><code>&lt;Information&gt; &lt;CID&gt;_whole_number_A_&lt;/CID&gt; &lt;string&gt;_text_that_is_not_useful_&lt;/string&gt; &lt;string&gt;_text_that_is_not_useful_&lt;/string&gt; &lt;string&gt;_PATTERN_A_&lt;/string&gt; &lt;string&gt;_text_that_is_not_useful_&lt;/string&gt; &lt;/Information&gt; &lt;Information&gt; &lt;CID&gt;_whole_number_B_&lt;/CID&gt; &lt;string&gt;_PATTERN_B_&lt;/string&gt; &lt;string&gt;_text_that_is_not_useful_&lt;/string&gt; &lt;string&gt;_text_that_is_not_useful_&lt;/string&gt; &lt;string&gt;_text_that_is_not_useful_&lt;/string&gt; &lt;string&gt;_text_that_is_not_useful_&lt;/string&gt; &lt;string&gt;_text_that_is_not_useful_&lt;/string&gt; &lt;/Information&gt; </code></pre> <p>Would like to awk to send the following pattern to a new file.</p> <pre><code>&lt;Information&gt; &lt;CID&gt;_whole_number_A_&lt;/CID&gt; &lt;string&gt;_PATTERN_A_&lt;/string&gt; &lt;/Information&gt; &lt;Information&gt; &lt;CID&gt;_whole_number_B_&lt;/CID&gt; &lt;string&gt;_PATTERN_B_&lt;/string&gt; &lt;/Information&gt; </code></pre> <p>Notes about the data:</p> <ul> <li>The file has 300,000+ CID items; each identified with a unique whole number.</li> <li>The PATTERNs (_PATTERN_A_, _PATTERN_B_, etc.) have the format UNII-&lt;10 characters>. For example: UNII-4J4Z8788N8 or UNII-12L95QD6KV.</li> <li>Not every CID has a UNII.</li> </ul> <p>Notes about my environment:</p> <ul> <li>Am working under Windows 7 and using the GnuWin32 utilities</li> </ul> <p>So, rephrasing in English:</p> <blockquote> <p>in FILE_1</p> <p>find every CID that has a UNII</p> <p>send the filtered results to FILE_2</p> </blockquote> <p>Thanks in advance for instructions.</p> <p>========================================================================</p> <p>OK, I'm doing something wrong.</p> <p>In my first implementation, the program only returns "record starts" and "closing tag," i.e.:</p> <pre><code>&lt;Information&gt; &lt;/Information&gt; </code></pre> <p>Here is how I applied your instructions.</p> <p>First, I'm running Windows so changed to FS="\r\n"</p> <p>The first regular expression is UNII, so changed to /UNII/.</p> <p>The second regular expression is CID, which you used in your instructions. I made no change there.</p> <p>For the second instance of PATTERN, I changed to /UNII/.</p> <p>Here is how my substitutions look:</p> <pre><code>BEGIN { RS="&lt;Information&gt;" FS="\r\n" } /UNII/ { print RS for (i=1;i&lt;NF;i++) { if ($i ~ /CID/ || $i ~ /UNII/) { print $i } } print "&lt;/Information&gt;" } </code></pre> <p>Because I am using Windows, I use a full path to execute the GnuWin32 utilities and read/write data. So my .bat file looks like this:</p> <pre><code>C:\bin\awk -f C:\bin\script.awk &lt; C:\Users\Owner\data\input_file.txt &gt; C:\Users\Owner\data\output_file.txt </code></pre> <p>What am I doing wrong?</p> <p>================================================================================= Here is sample data:</p> <pre><code>&lt;Information&gt; &lt;CID&gt;1&lt;/CID&gt; &lt;Synonym&gt;Acetyl carnitine&lt;/Synonym&gt; &lt;Synonym&gt;O-Acetyl-L-carnitine&lt;/Synonym&gt; &lt;Synonym&gt;Ammonium, (3-carboxy-2-hydroxypropyl)trimethyl-, hydroxide, inner salt, acetate, DL-&lt;/Synonym&gt; &lt;Synonym&gt;UNII-07OP6H4V4A&lt;/Synonym&gt; &lt;Synonym&gt;_20+_more_&lt;/Synonym&gt; &lt;/Information&gt; &lt;Information&gt; &lt;CID&gt;10006&lt;/CID&gt; &lt;Synonym&gt;HYDANTOIN&lt;/Synonym&gt; &lt;Synonym&gt;UNII-I6208298TA&lt;/Synonym&gt; &lt;Synonym&gt;53760_FLUKA&lt;/Synonym&gt; &lt;Synonym&gt;NSC9226&lt;/Synonym&gt; &lt;Synonym&gt;_20+_more_&lt;/Synonym&gt; &lt;/Information&gt; &lt;Information&gt; &lt;CID&gt;10007&lt;/CID&gt; &lt;Synonym&gt;Lucofen SA&lt;/Synonym&gt; &lt;Synonym&gt;461-78-9&lt;/Synonym&gt; &lt;Synonym&gt;EINECS 207-314-9&lt;/Synonym&gt; &lt;Synonym&gt;STK664067&lt;/Synonym&gt; &lt;Synonym&gt;DEA No. 1645&lt;/Synonym&gt; &lt;Synonym&gt;UNII-NHW07912O7&lt;/Synonym&gt; &lt;Synonym&gt;CHEMBL1201269&lt;/Synonym&gt; &lt;Synonym&gt;HMS1376E21&lt;/Synonym&gt; &lt;Synonym&gt;_20+_more_&lt;/Synonym&gt; &lt;/Information&gt; </code></pre>
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