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bio:tools:codonopttable [2010/02/15 10:16]
172.26.0.166
bio:tools:codonopttable [2010/06/30 19:52] (current)
172.26.15.75
Line 70: Line 70:
 Here is a python script that provides a Graphical User Interface: Here is a python script that provides a Graphical User Interface:
 You need to have wxpython installed on your system. You need to have wxpython installed on your system.
-<file>+<code python>
 #!/usr/bin/python #!/usr/bin/python
 import wx import wx
 import os import os
 import random import random
 +import re
 class testgui(wx.Frame): class testgui(wx.Frame):
     def __init__(self, parent, id, title):     def __init__(self, parent, id, title):
-        wx.Frame.__init__(self, parent, id, title, size=(600,300))+        wx.Frame.__init__(self, parent, id, title, size=(683,360))
         # Menu stuff         # Menu stuff
         menubar =wx.MenuBar()         menubar =wx.MenuBar()
Line 90: Line 91:
         panel =wx.Panel(self, -1)         panel =wx.Panel(self, -1)
         hbsizer =wx.BoxSizer(wx.VERTICAL)         hbsizer =wx.BoxSizer(wx.VERTICAL)
-        self.orig_text =wx.TextCtrl(panel,-1,size=(250,150),style=wx.TE_MULTILINE)+        self.orig_text =wx.TextCtrl(panel,-1,size=(679,275),style=wx.TE_MULTILINE)
        # self.orig_text =wx.TextCtrl(panel,-1)        # self.orig_text =wx.TextCtrl(panel,-1)
-#Objects+       #Objects
         self.orig_label =wx.StaticText(panel,-1, 'Paste Your Sequence here:')         self.orig_label =wx.StaticText(panel,-1, 'Paste Your Sequence here:')
- ok_button =wx.Button(panel,-1,'Run CodonOptTable'+        ok_button =wx.Button(panel,-1,'Run CodonOptTable'
- cancel_button =wx.Button(panel,-1,'Clear'+        cancel_button =wx.Button(panel,-1,'Clear'
- exit_button=wx.Button(panel,-1,'Exit'+        format_seq =wx.Button(panel,-1,'Format Seq'
- disp =wx.StaticText(panel,-1,''+        rhead =wx.Button(panel,-1,'Remove Header'
-  +        exit_button=wx.Button(panel,-1,'Exit'
- vsizer1 =wx.BoxSizer(wx.HORIZONTAL) +        disp =wx.StaticText(panel,-1,''
- vsizer4 =wx.BoxSizer(wx.HORIZONTAL) +     vsizer1 =wx.BoxSizer(wx.HORIZONTAL) 
- vsizer5 =wx.BoxSizer(wx.HORIZONTAL) +     vsizer4 =wx.BoxSizer(wx.HORIZONTAL) 
- vsizer6 =wx.BoxSizer(wx.HORIZONTAL) +     vsizer5 =wx.BoxSizer(wx.HORIZONTAL) 
- vsizer2 =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) +     vsizer1.Add(self.orig_label,1,wx.CENTRE,10) 
-  +     vsizer2.Add(self.orig_text,1,wx.CENTRE,10) 
- vsizer5.Add(ok_button,1,wx.RIGHT,1) +  
- vsizer5.Add(cancel_button,1,wx.RIGHT,1) +     vsizer5.Add(rhead,1,wx.RIGHT,1) 
- vsizer5.Add(exit_button,1,wx.RIGHT,1) +      vsizer5.Add(format_seq,1,wx.RIGHT,1) 
-  +      vsizer5.Add(ok_button,1,wx.RIGHT,1) 
- vsizer6.Add(disp,1,wx.CENTER,1) +     vsizer5.Add(cancel_button,1,wx.RIGHT,1) 
-  +     vsizer5.Add(exit_button,1,wx.RIGHT,1) 
- hbsizer.Add(vsizer1,0,wx.CENTER|wx.ALL,1) +  
-# hbsizer.Add(self.orig_text,0, wx.CENTER|wx.ALL,1) +     vsizer6.Add(disp,1,wx.CENTER,1) 
- hbsizer.Add(vsizer2,0, wx.CENTER|wx.ALL,1) +  
- hbsizer.Add(vsizer4,0, wx.CENTER|wx.ALL,1) +     hbsizer.Add(vsizer1,0,wx.CENTER|wx.ALL,1) 
- hbsizer.Add(vsizer5,0,wx.ALIGN_RIGHT|wx.RIGHT,1) +       hbsizer.Add(self.orig_text,0, wx.CENTER|wx.ALL,1) 
- hbsizer.Add(vsizer6,0,wx.CENTER,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  #events
- self.Bind(wx.EVT_BUTTON,self.executa,ok_button) +      self.Bind(wx.EVT_BUTTON,self.executa,ok_button) 
- self.Bind(wx.EVT_MENU, self.soja, exitmenu) +     self.Bind(wx.EVT_BUTTON,self.rheader,rhead) 
- self.Bind(wx.EVT_BUTTON,self.clear,cancel_button) +      self.Bind(wx.EVT_BUTTON,self.format_seq,format_seq) 
- self.Bind(wx.EVT_BUTTON,self.soja,exit_button) +      self.Bind(wx.EVT_MENU, self.soja, exitmenu) 
- #panel.CreateStatusBar() +     self.Bind(wx.EVT_BUTTON,self.clear,cancel_button) 
- panel.SetSizer(hbsizer)  +     self.Bind(wx.EVT_BUTTON,self.soja,exit_button) 
- self.Centre() +#pane l.CreateStatusBar() 
- +     panel.SetSizer(hbsizer)  
-        self.Show(True)+     self.Centre() 
 +     self.Show(True)
     def clear(self,event=None):     def clear(self,event=None):
  self.orig_text.SetValue('')  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):     def soja(self, event=None):
-        self.Close(True)+    self.Close(True)
     def executa(self,event=None):     def executa(self,event=None):
  recordid=random.randint(20,10055)  recordid=random.randint(20,10055)
Line 144: Line 156:
 testgui(None, -1, 'CodonOptTable GUI') testgui(None, -1, 'CodonOptTable GUI')
 app.MainLoop() 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> </codeThis will grep only the part of matching line that matching the pattern eg How many occurence of "ATCG"  in a sequence?
bio/tools/codonopttable.1266228962.txt.gz · Last modified: 2010/05/22 14:19 (external edit)