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--- bio:tools:codonopttable [2010/02/15 10:16] – 172.26.0.166
+++ bio:tools:codonopttable [2010/05/22 14:19] – external edit 127.0.0.1
@@ Line 70: / Line 70: @@
 Here is a python script that provides a Graphical User Interface:
 You need to have wxpython installed on your system.
-<file>
+<code python>
 #!/usr/bin/python
 import wx
@@ Line 144: / Line 144: @@
 testgui(None, -1, 'CodonOptTable GUI')
 app.MainLoop()
-</file>
+</code>
+This is used together with the perl script:
+<code perl>#!/bin/perl
+use Bio::Tools::CodonOptTable;
+$sequence = $ARGV[0];
+sub codon {
+my ($mysequence)=@_;
+print $mysequence;
+my $seqobj = Bio::Tools::CodonOptTable->new ( -seq => $mysequence,
+                                                -id  => 'GeneFragment-12',
+                                                -accession_number => 'Myseq1',
+                                                -alphabet => 'dna',
+                                                -is_circular => 1,
+                                                -genetic_code => 1,
+                                   );
+#my $seqobj = Bio::Tools::CodonOptTable->new(-file => $mysequence,
+#
+#                                             -format => 'Fasta',
+#                                             -genetic_code => 1,
+#                                             );
+my $myCodons = $seqobj->rscu_rac_table();
+if($myCodons)
+        {
+            for my $each_aa (@$myCodons)
+        {
+        print "Codon      : ",$each_aa->{'codon'},"\t";
+        print "Frequency  : ",$each_aa->{'frequency'},"\t";
+        print "AminoAcid  : ",$each_aa->{'aa_name'},"\t";
+        print "RSCU Value : ",$each_aa->{'rscu'},"\t"; #Relative Synonymous Codons Uses
+        print "RAC Value  : ",$each_aa->{'rac'},"\t"; #Relative Adaptiveness of a Codon
+        print "\n";
+        }
+        }
+ while ( my ($amino_acid, $codon) = each(%$prefered_codons) ) {
+print "AminoAcid : $amino_acid \t Codon : $codon\n"; }
+$seqobj->generate_graph($myCodons,"/home/obiero/codonopt/myoutput.gif");
+}
+codon($sequence); </code>
+<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?