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comparison fasta-tool.pl @ 1:d0a9360bb58e draft

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author lz_hust
date Fri, 31 May 2019 23:08:21 -0400
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750 <td id="LC1" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>!/usr/bin/perl -w</span></td>
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759 <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 &lt;FASTA file&gt; &lt;output file&gt;</span></td>
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761 <tr>
762 <td id="L4" class="blob-num js-line-number" data-line-number="4"></td>
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774 <tr>
775 <td id="L7" class="blob-num js-line-number" data-line-number="7"></td>
776 <td id="LC7" class="blob-code blob-code-inner js-file-line"><span class="pl-k">while</span> (&lt;IN&gt;) {</td>
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778 <tr>
779 <td id="L8" class="blob-num js-line-number" data-line-number="8"></td>
780 <td id="LC8" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">chop</span>;</td>
781 </tr>
782 <tr>
783 <td id="L9" class="blob-num js-line-number" data-line-number="9"></td>
784 <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>^&gt;<span class="pl-pds">/</span></span>) {</td>
785 </tr>
786 <tr>
787 <td id="L10" class="blob-num js-line-number" data-line-number="10"></td>
788 <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>^&gt;</span><span class="pl-sr"><span class="pl-pds">//</span></span>;</td>
789 </tr>
790 <tr>
791 <td id="L11" class="blob-num js-line-number" data-line-number="11"></td>
792 <td id="LC11" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> (<span class="pl-smi">$.</span> &gt; 1) {</td>
793 </tr>
794 <tr>
795 <td id="L12" class="blob-num js-line-number" data-line-number="12"></td>
796 <td id="LC12" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span> OUT <span class="pl-c1">sprintf</span>(<span class="pl-s"><span class="pl-pds">&quot;</span>%.3f<span class="pl-pds">&quot;</span></span>, <span class="pl-smi">$gc</span>/<span class="pl-smi">$length</span>) . <span class="pl-s"><span class="pl-pds">&quot;</span><span class="pl-cce">\n</span><span class="pl-pds">&quot;</span></span>;</td>
797 </tr>
798 <tr>
799 <td id="L13" class="blob-num js-line-number" data-line-number="13"></td>
800 <td id="LC13" class="blob-code blob-code-inner js-file-line"> }</td>
801 </tr>
802 <tr>
803 <td id="L14" class="blob-num js-line-number" data-line-number="14"></td>
804 <td id="LC14" class="blob-code blob-code-inner js-file-line"> <span class="pl-smi">$gc</span> = 0;</td>
805 </tr>
806 <tr>
807 <td id="L15" class="blob-num js-line-number" data-line-number="15"></td>
808 <td id="LC15" class="blob-code blob-code-inner js-file-line"> <span class="pl-smi">$length</span> = 0;</td>
809 </tr>
810 <tr>
811 <td id="L16" class="blob-num js-line-number" data-line-number="16"></td>
812 <td id="LC16" class="blob-code blob-code-inner js-file-line"> } <span class="pl-k">else</span> {</td>
813 </tr>
814 <tr>
815 <td id="L17" class="blob-num js-line-number" data-line-number="17"></td>
816 <td id="LC17" class="blob-code blob-code-inner js-file-line"> ++<span class="pl-smi">$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>
817 </tr>
818 <tr>
819 <td id="L18" class="blob-num js-line-number" data-line-number="18"></td>
820 <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>
821 </tr>
822 <tr>
823 <td id="L19" class="blob-num js-line-number" data-line-number="19"></td>
824 <td id="LC19" class="blob-code blob-code-inner js-file-line"> }</td>
825 </tr>
826 <tr>
827 <td id="L20" class="blob-num js-line-number" data-line-number="20"></td>
828 <td id="LC20" class="blob-code blob-code-inner js-file-line">}</td>
829 </tr>
830 <tr>
831 <td id="L21" class="blob-num js-line-number" data-line-number="21"></td>
832 <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">&quot;</span>%.3f<span class="pl-pds">&quot;</span></span>, <span class="pl-smi">$gc</span>/<span class="pl-smi">$length</span>) . <span class="pl-s"><span class="pl-pds">&quot;</span><span class="pl-cce">\n</span><span class="pl-pds">&quot;</span></span>;</td>
833 </tr>
834 <tr>
835 <td id="L22" class="blob-num js-line-number" data-line-number="22"></td>
836 <td id="LC22" class="blob-code blob-code-inner js-file-line"><span class="pl-c1">close</span>( IN );</td>
837 </tr>
838 <tr>
839 <td id="L23" class="blob-num js-line-number" data-line-number="23"></td>
840 <td id="LC23" class="blob-code blob-code-inner js-file-line"><span class="pl-c1">close</span>( OUT );</td>
841 </tr>
842 </table>
843
844 <details class="details-reset details-overlay BlobToolbar position-absolute js-file-line-actions dropdown d-none" aria-hidden="true">
845 <summary class="btn-octicon ml-0 px-2 p-0 bg-white border border-gray-dark rounded-1" aria-label="Inline file action toolbar">
846 <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 0 0 3zM13 7.5a1.5 1.5 0 1 1-3 0 1.5 1.5 0 0 1 3 0z"/></svg>
847 </summary>
848 <details-menu>
849 <ul class="BlobToolbar-dropdown dropdown-menu dropdown-menu-se mt-2" style="width:185px">
850 <li><clipboard-copy role="menuitem" class="dropdown-item" id="js-copy-lines" style="cursor:pointer;" data-original-text="Copy lines">Copy lines</clipboard-copy></li>
851 <li><clipboard-copy role="menuitem" class="dropdown-item" id="js-copy-permalink" style="cursor:pointer;" data-original-text="Copy permalink">Copy permalink</clipboard-copy></li>
852 <li><a class="dropdown-item js-update-url-with-hash" id="js-view-git-blame" role="menuitem" href="/huster16/fasta-tool/blame/7bdf0b29c9176862290c43996ac35696c746b463/fasta-tool.pl">View git blame</a></li>
853 <li><a class="dropdown-item" id="js-new-issue" role="menuitem" href="/huster16/fasta-tool/issues/new">Reference in new issue</a></li>
854 </ul>
855 </details-menu>
856 </details>
857
858 </div>
859
860 </div>
861
862
863
864 <details class="details-reset details-overlay details-overlay-dark">
865 <summary data-hotkey="l" aria-label="Jump to line"></summary>
866 <details-dialog class="Box Box--overlay d-flex flex-column anim-fade-in fast linejump" aria-label="Jump to line">
867 <!-- '"` --><!-- </textarea></xmp> --></option></form><form class="js-jump-to-line-form Box-body d-flex" action="" accept-charset="UTF-8" method="get"><input name="utf8" type="hidden" value="&#x2713;" />
868 <input class="form-control flex-auto mr-3 linejump-input js-jump-to-line-field" type="text" placeholder="Jump to line&hellip;" aria-label="Jump to line" autofocus>
869 <button type="submit" class="btn" data-close-dialog>Go</button>
870 </form> </details-dialog>
871 </details>
872
873
874
875 </div>
876 <div class="modal-backdrop js-touch-events"></div>
877 </div>
878
879 </main>
880 </div>
881
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883 </div>
884
885
886 <div class="footer container-lg width-full p-responsive" role="contentinfo">
887 <div class="position-relative d-flex flex-row-reverse flex-lg-row flex-wrap flex-lg-nowrap flex-justify-center flex-lg-justify-between pt-6 pb-2 mt-6 f6 text-gray border-top border-gray-light ">
888 <ul class="list-style-none d-flex flex-wrap col-12 col-lg-5 flex-justify-center flex-lg-justify-between mb-2 mb-lg-0">
889 <li class="mr-3 mr-lg-0">&copy; 2019 <span title="0.20779s from unicorn-557998b5d7-n7n6p">GitHub</span>, Inc.</li>
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896
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898 <svg height="24" class="octicon octicon-mark-github" viewBox="0 0 16 16" version="1.1" width="24" aria-hidden="true"><path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z"/></svg>
899 </a>
900 <ul class="list-style-none d-flex flex-wrap col-12 col-lg-5 flex-justify-center flex-lg-justify-between mb-2 mb-lg-0">
901 <li class="mr-3 mr-lg-0"><a data-ga-click="Footer, go to contact, text:contact" href="https://github.com/contact">Contact GitHub</a></li>
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907
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910 <div class="d-flex flex-justify-center pb-6">
911 <span class="f6 text-gray-light"></span>
912 </div>
913 </div>
914
915
916
917 <div id="ajax-error-message" class="ajax-error-message flash flash-error">
918 <svg class="octicon octicon-alert" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.893 1.5c-.183-.31-.52-.5-.887-.5s-.703.19-.886.5L.138 13.499a.98.98 0 0 0 0 1.001c.193.31.53.501.886.501h13.964c.367 0 .704-.19.877-.5a1.03 1.03 0 0 0 .01-1.002L8.893 1.5zm.133 11.497H6.987v-2.003h2.039v2.003zm0-3.004H6.987V5.987h2.039v4.006z"/></svg>
919 <button type="button" class="flash-close js-ajax-error-dismiss" aria-label="Dismiss error">
920 <svg class="octicon octicon-x" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48L7.48 8z"/></svg>
921 </button>
922 You can’t perform that action at this time.
923 </div>
924
925
926 <script crossorigin="anonymous" integrity="sha512-EPrD+nddbyhpiLL8l3M8VfJpZr4J2EWQLaPXZ+6A3VDJKzS5HeZ3dkMVieHSdvIPHsMbWPyVlY42SWKoS4XTfA==" type="application/javascript" src="https://github.githubassets.com/assets/compat-bootstrap-831f12d4.js"></script>
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930
931
932
933 <div class="js-stale-session-flash stale-session-flash flash flash-warn flash-banner" hidden
934 >
935 <svg class="octicon octicon-alert" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.893 1.5c-.183-.31-.52-.5-.887-.5s-.703.19-.886.5L.138 13.499a.98.98 0 0 0 0 1.001c.193.31.53.501.886.501h13.964c.367 0 .704-.19.877-.5a1.03 1.03 0 0 0 .01-1.002L8.893 1.5zm.133 11.497H6.987v-2.003h2.039v2.003zm0-3.004H6.987V5.987h2.039v4.006z"/></svg>
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937 <span class="signed-out-tab-flash">You signed out in another tab or window. <a href="">Reload</a> to refresh your session.</span>
938 </div>
939 <template id="site-details-dialog">
940 <details class="details-reset details-overlay details-overlay-dark lh-default text-gray-dark hx_rsm" open>
941 <summary role="button" aria-label="Close dialog"></summary>
942 <details-dialog class="Box Box--overlay d-flex flex-column anim-fade-in fast hx_rsm-dialog hx_rsm-modal">
943 <button class="Box-btn-octicon m-0 btn-octicon position-absolute right-0 top-0" type="button" aria-label="Close dialog" data-close-dialog>
944 <svg class="octicon octicon-x" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48L7.48 8z"/></svg>
945 </button>
946 <div class="octocat-spinner my-6 js-details-dialog-spinner"></div>
947 </details-dialog>
948 </details>
949 </template>
950
951 <div class="Popover js-hovercard-content position-absolute" style="display: none; outline: none;" tabindex="0">
952 <div class="Popover-message Popover-message--bottom-left Popover-message--large Box box-shadow-large" style="width:360px;">
953 </div>
954 </div>
955
956 <div aria-live="polite" class="js-global-screen-reader-notice sr-only"></div>
957
958 </body>
959 </html>
960