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| author | lz_hust |
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| date | Fri, 31 May 2019 23:08:21 -0400 |
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<td id="L2" class="blob-num js-line-number" data-line-number="2"></td> <td id="LC2" class="blob-code blob-code-inner js-file-line"> </td> </tr> <tr> <td id="L3" class="blob-num js-line-number" data-line-number="3"></td> <td id="LC3" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> usage : perl toolExample.pl <FASTA file> <output file></span></td> </tr> <tr> <td id="L4" class="blob-num js-line-number" data-line-number="4"></td> <td id="LC4" class="blob-code blob-code-inner js-file-line"> </td> </tr> <tr> <td id="L5" class="blob-num js-line-number" data-line-number="5"></td> <td id="LC5" class="blob-code blob-code-inner js-file-line"><span class="pl-c1">open</span> (IN, <span class="pl-s"><span class="pl-pds">"</span><<span class="pl-smi">$ARGV</span>[0]<span class="pl-pds">"</span></span>);</td> </tr> <tr> <td id="L6" class="blob-num js-line-number" data-line-number="6"></td> <td id="LC6" class="blob-code blob-code-inner js-file-line"><span class="pl-c1">open</span> (OUT, <span class="pl-s"><span class="pl-pds">"</span>><span class="pl-smi">$ARGV</span>[1]<span class="pl-pds">"</span></span>);</td> </tr> <tr> <td id="L7" class="blob-num js-line-number" data-line-number="7"></td> <td id="LC7" class="blob-code blob-code-inner js-file-line"><span class="pl-k">while</span> (<IN>) {</td> </tr> <tr> <td id="L8" class="blob-num js-line-number" data-line-number="8"></td> <td id="LC8" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">chop</span>;</td> </tr> <tr> <td id="L9" class="blob-num js-line-number" data-line-number="9"></td> <td id="LC9" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> (<span class="pl-sr"><span class="pl-pds"><span class="pl-c1">m</span>/</span>^><span class="pl-pds">/</span></span>) {</td> </tr> <tr> <td id="L10" class="blob-num js-line-number" data-line-number="10"></td> <td id="LC10" class="blob-code blob-code-inner js-file-line"> <span class="pl-sr"><span class="pl-pds"><span class="pl-c1">s</span>/</span>^></span><span class="pl-sr"><span class="pl-pds">//</span></span>;</td> </tr> <tr> <td id="L11" class="blob-num js-line-number" data-line-number="11"></td> <td id="LC11" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> (<span class="pl-smi">$.</span> > 1) {</td> </tr> <tr> <td id="L12" class="blob-num js-line-number" data-line-number="12"></td> <td id="LC12" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span> OUT <span class="pl-c1">sprintf</span>(<span class="pl-s"><span class="pl-pds">"</span>%.3f<span class="pl-pds">"</span></span>, <span class="pl-smi">$gc</span>/<span class="pl-smi">$length</span>) . <span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</td> </tr> <tr> <td id="L13" class="blob-num js-line-number" data-line-number="13"></td> <td id="LC13" class="blob-code blob-code-inner js-file-line"> }</td> </tr> <tr> <td id="L14" class="blob-num js-line-number" data-line-number="14"></td> <td id="LC14" class="blob-code blob-code-inner js-file-line"> <span class="pl-smi">$gc</span> = 0;</td> </tr> <tr> <td id="L15" class="blob-num js-line-number" data-line-number="15"></td> <td id="LC15" class="blob-code blob-code-inner js-file-line"> <span class="pl-smi">$length</span> = 0;</td> </tr> <tr> <td id="L16" class="blob-num js-line-number" data-line-number="16"></td> <td id="LC16" class="blob-code blob-code-inner js-file-line"> } <span class="pl-k">else</span> {</td> </tr> <tr> <td id="L17" class="blob-num js-line-number" data-line-number="17"></td> <td id="LC17" class="blob-code blob-code-inner js-file-line"> ++<span class="pl-smi">$gc</span> <span class="pl-k">while</span> <span class="pl-sr"><span class="pl-pds"><span class="pl-c1">m</span>/</span><span class="pl-c1">[gc]</span><span class="pl-pds">/</span></span><span class="pl-sr"><span class="pl-pds"><span class="pl-k">ig</span></span></span>;</td> </tr> <tr> <td id="L18" class="blob-num js-line-number" data-line-number="18"></td> <td id="LC18" class="blob-code blob-code-inner js-file-line"> <span class="pl-smi">$length</span> += <span class="pl-c1">length</span> <span class="pl-smi">$_</span>;</td> </tr> <tr> <td id="L19" class="blob-num js-line-number" data-line-number="19"></td> <td id="LC19" class="blob-code blob-code-inner js-file-line"> }</td> </tr> <tr> <td id="L20" class="blob-num js-line-number" data-line-number="20"></td> <td id="LC20" class="blob-code blob-code-inner js-file-line">}</td> </tr> <tr> <td id="L21" class="blob-num js-line-number" data-line-number="21"></td> <td id="LC21" class="blob-code blob-code-inner js-file-line"><span class="pl-c1">print</span> OUT <span class="pl-c1">sprintf</span>(<span class="pl-s"><span class="pl-pds">"</span>%.3f<span class="pl-pds">"</span></span>, <span class="pl-smi">$gc</span>/<span class="pl-smi">$length</span>) . <span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</td> </tr> <tr> <td id="L22" class="blob-num js-line-number" data-line-number="22"></td> <td id="LC22" class="blob-code blob-code-inner js-file-line"><span class="pl-c1">close</span>( IN );</td> </tr> <tr> <td id="L23" class="blob-num js-line-number" data-line-number="23"></td> <td id="LC23" class="blob-code blob-code-inner js-file-line"><span class="pl-c1">close</span>( OUT );</td> </tr> </table> <details class="details-reset details-overlay BlobToolbar position-absolute js-file-line-actions dropdown d-none" aria-hidden="true"> <summary class="btn-octicon ml-0 px-2 p-0 bg-white border border-gray-dark rounded-1" aria-label="Inline file action toolbar"> <svg class="octicon octicon-kebab-horizontal" viewBox="0 0 13 16" version="1.1" width="13" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M1.5 9a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3zm5 0a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 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