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bio:tools:codonopttable [2009/12/17 09:48]
172.26.15.75
bio:tools:codonopttable [2010/06/30 19:52] (current)
172.26.15.75
Line 66: Line 66:
 <code> <code>
 $seqobj->generate_graph($myCodons,"myoutput.gif");</code> $seqobj->generate_graph($myCodons,"myoutput.gif");</code>
- 
 ====Creating a gui for CodonOptTable==== ====Creating a gui for CodonOptTable====
  
 +Here is a python script that provides a Graphical User Interface:
 +You need to have wxpython installed on your system.
 +<code python>
 +#!/usr/bin/python
 +import wx
 +import os
 +import random
 +import re
 +class testgui(wx.Frame):
 +    def __init__(self, parent, id, title):
 +        wx.Frame.__init__(self, parent, id, title, size=(683,360))
 +        # Menu stuff
 +        menubar =wx.MenuBar()
 +        menufile =wx.Menu()
 +        menuhelp =wx.Menu()
 +        self.SetMenuBar(menubar)
 +        menubar.Append(menufile, '&File')
 +        menubar.Append(menuhelp, '&Help')
 +        exitmenu =menufile.Append(-1, 'Quit', 'Exit Application')
 +        about =menuhelp.Append(-1, 'About', 'About us')
 +        #panel creation and sizer
 +        panel =wx.Panel(self, -1)
 +        hbsizer =wx.BoxSizer(wx.VERTICAL)
 +        self.orig_text =wx.TextCtrl(panel,-1,size=(679,275),style=wx.TE_MULTILINE)
 +       # self.orig_text =wx.TextCtrl(panel,-1)
 +       #Objects
 +        self.orig_label =wx.StaticText(panel,-1, 'Paste Your Sequence here:')
 +        ok_button =wx.Button(panel,-1,'Run CodonOptTable')
 +        cancel_button =wx.Button(panel,-1,'Clear')
 +        format_seq =wx.Button(panel,-1,'Format Seq')
 +        rhead =wx.Button(panel,-1,'Remove Header')
 +        exit_button=wx.Button(panel,-1,'Exit')
 +        disp =wx.StaticText(panel,-1,'')
 +      vsizer1 =wx.BoxSizer(wx.HORIZONTAL)
 +      vsizer4 =wx.BoxSizer(wx.HORIZONTAL)
 +      vsizer5 =wx.BoxSizer(wx.HORIZONTAL)
 +      vsizer6 =wx.BoxSizer(wx.HORIZONTAL)
 +      vsizer2 =wx.BoxSizer(wx.HORIZONTAL)
 + 
 +      vsizer1.Add(self.orig_label,1,wx.CENTRE,10)
 +      vsizer2.Add(self.orig_text,1,wx.CENTRE,10)
 + 
 +      vsizer5.Add(rhead,1,wx.RIGHT,1)
 +      vsizer5.Add(format_seq,1,wx.RIGHT,1)
 +      vsizer5.Add(ok_button,1,wx.RIGHT,1)
 +      vsizer5.Add(cancel_button,1,wx.RIGHT,1)
 +      vsizer5.Add(exit_button,1,wx.RIGHT,1)
 + 
 +      vsizer6.Add(disp,1,wx.CENTER,1)
 + 
 +      hbsizer.Add(vsizer1,0,wx.CENTER|wx.ALL,1)
 +#       hbsizer.Add(self.orig_text,0, wx.CENTER|wx.ALL,1)
 +      hbsizer.Add(vsizer2,0, wx.CENTER|wx.ALL,1)
 +      hbsizer.Add(vsizer4,0, wx.CENTER|wx.ALL,1)
 +      hbsizer.Add(vsizer5,0,wx.ALIGN_RIGHT|wx.RIGHT,1)
 +      hbsizer.Add(vsizer6,0,wx.CENTER,1)
 + 
 + #events
 +      self.Bind(wx.EVT_BUTTON,self.executa,ok_button)
 +      self.Bind(wx.EVT_BUTTON,self.rheader,rhead)
 +      self.Bind(wx.EVT_BUTTON,self.format_seq,format_seq)
 +      self.Bind(wx.EVT_MENU, self.soja, exitmenu)
 +      self.Bind(wx.EVT_BUTTON,self.clear,cancel_button)
 +      self.Bind(wx.EVT_BUTTON,self.soja,exit_button)
 +#pane l.CreateStatusBar()
 +      panel.SetSizer(hbsizer) 
 +      self.Centre()
 +      self.Show(True)
 +    def clear(self,event=None):
 + self.orig_text.SetValue('')
 +    def format_seq(self,event=None):
 + originator=self.orig_text.GetValue()
 + comm=re.sub('[ \t\r\n]','',originator)
 +        self.orig_text.SetValue(comm)
 +    def rheader(self,event=None):
 + originator=self.orig_text.GetValue()
 + comm=re.sub('>.*','>',originator)
 +        self.orig_text.SetValue(comm)
 +    def soja(self, event=None):
 +    self.Close(True)
 +    def executa(self,event=None):
 + recordid=random.randint(20,10055)
 + originator=self.orig_text.GetValue()
 + os.system('perl /home/obiero/codonopt/codonOpt-test.pl %s' %originator)
 + wx.MessageBox('DONE! check the output in you folder', 'CodonOptTable Info'   
 +app =wx.App()
 +testgui(None, -1, 'CodonOptTable GUI')
 +app.MainLoop()
 +
 +</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?
bio/tools/codonopttable.1261043303.txt.gz · Last modified: 2010/05/22 14:19 (external edit)