Differences

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--- bio:tools:codonopttable [2010/02/15 10:21] – 172.26.0.166
+++ bio:tools:codonopttable [2010/05/22 14:19] – external edit 127.0.0.1
@@ Line 144: / Line 144: @@
 testgui(None, -1, 'CodonOptTable GUI')
 app.MainLoop()
-</code python>
+</code>
-This is used with the perl script:
+This is used together with the perl script:
 <code perl>#!/bin/perl
 use Bio::Tools::CodonOptTable;
@@ Line 185: / Line 185: @@
 $seqobj->generate_graph($myCodons,"/home/obiero/codonopt/myoutput.gif");
 }
-codon($sequence); </code perl>
+codon($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?