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POfind unique first top and bottom lines of fastq file from fasta file
 

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    <p>I have 2 files one is <code>fasta</code> file and other one is <code>fastq</code> file. I want to take the <code>fasta</code>, read each line and search each line in the <code>fastq</code> file and print top line and bottom lines. This is what I have</p> <p><strong>fasta file</strong></p> <blockquote> <p>read1</p> <p>AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA</p> <p>AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAC</p> <p>AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG</p> <p>AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGA</p> <p>AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGG</p> </blockquote> <pre><code>for seq in `cat sequences`;do grep -A 2 -B 1 $seq FAP.1.txt;done </code></pre> <blockquote> <p>@DH1DQQN1:269:C1UKCACXX:1:1107:20386:6577 1:N:0:TTAGGC</p> <p>AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAC</p> <p>+</p> <p>CCCFFFFFHGHHHJIJHFDDDB173@8815BDDB###############</p> <p>@DH1DQQN1:269:C1UKCACXX:1:1114:5718:53821 1:N:0:TTAGGC</p> <p>AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA</p> <p>+ ;@?DBD&lt;@@FFHHH&lt; <p>@DH1DQQN1:269:C1UKCACXX:1:1209:10703:35361 1:N:0:TTAGGC</p> <p>AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA</p> <p>+</p> <p>@@@FFFFFHGHHHGIJHFDDDDDBDD69@6B-707537BDDDB75@@85</p> <p>@DH1DQQN1:269:C1UKCACXX:1:1210:18926:75163 1:N:0:TTAGGC</p> <p>AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG</p> <p>@CCFFFFFHHHHHJJJHFDDD@77BDDDDB077007@B###########</p> </blockquote> <p>From this we can see that <code>AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA</code> appeared twice, but I want to print only once. how can I do that?</p> <p><strong>Final output file</strong></p> <blockquote> <p>@DH1DQQN1:269:C1UKCACXX:1:1107:20386:6577 1:N:0:TTAGGC</p> <p>AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAC</p> <p>+</p> <p>CCCFFFFFHGHHHJIJHFDDDB173@8815BDDB###############</p> <p>@DH1DQQN1:269:C1UKCACXX:1:1114:5718:53821 1:N:0:TTAGGC</p> <p>AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA</p> <p>+</p> <p>;@?DBD&lt;@@FFHHH&lt; <p>@DH1DQQN1:269:C1UKCACXX:1:1210:18926:75163 1:N:0:TTAGGC</p> <p>AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG</p> <p>+</p> <p>@CCFFFFFHHHHHJJJHFDDD@77BDDDDB077007@B</p> </blockquote>
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    1. COWhat is it with you biologist.. always post the worst formatted questions! You need to read http://stackoverflow.com/help/formatting to understand how the formatting works on Stackoverflow and http://stackoverflow.com/help/asking on asking a question.
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    2. COsorry for this!next time won't do that
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    3. COYou have asked 14 questions over the last couple of months and all of them where terrible formatted and had to be completely overhauled *(mostly by me it seems)*. If you expect the community to help you then the least you can do is properly formatting your questions.
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