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bio:tools:codonopttable

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bio:tools:codonopttable [2010/02/15 10:24] – 172.26.0.166bio:tools:codonopttable [2010/05/22 14:19] – external edit 127.0.0.1
Line 145: Line 145:
 app.MainLoop() app.MainLoop()
 </code> </code>
-This is used with the perl script:+This is used together with the perl script:
 <code perl>#!/bin/perl <code perl>#!/bin/perl
 use Bio::Tools::CodonOptTable; use Bio::Tools::CodonOptTable;
Line 186: Line 186:
 } }
 codon($sequence); </code> codon($sequence); </code>
-Note:+<note warning> Note: You have to edit the paths to suite your setup. </note> 
 +==== Usefull ReGex ==== 
 +---- 
 +Merge sequence lines using sed:  
 + 
 +<code>$ grep -v Tp sequence | tr -d "\n" > new_sequence_file</code> 
 + 
 +<code>$ grep -o <pattern> </code> This will grep only the part of matching line that matching the pattern eg How many occurence of "ATCG"  in a sequence?
bio/tools/codonopttable.txt · Last modified: 2010/06/30 19:52 by 172.26.15.75