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bio:tools:codonopttable [2009/12/17 09:42] – 172.26.15.75bio:tools:codonopttable [2009/12/17 09:47] – 172.26.15.75
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 http://search.cpan.org/~shardiwal/Bio-Tools-CodonOptTable-0.07/lib/Bio/Tools/CodonOptTable.pm http://search.cpan.org/~shardiwal/Bio-Tools-CodonOptTable-0.07/lib/Bio/Tools/CodonOptTable.pm
  
-Uses /Examples +====USES or Examples====
-USES or Examples+
  
 You can use this module in the following ways You can use this module in the following ways
 +<code>
 use Bio::Tools::CodonOptTable; use Bio::Tools::CodonOptTable;
  
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                                                 -genetic_code => 1,                                                 -genetic_code => 1,
                                    );                                    );
 +</code>
 B<#If you wanna read from file> B<#If you wanna read from file>
 +<code>
 my $seqobj = Bio::Tools::CodonOptTable->new(-file => "contig.fasta", my $seqobj = Bio::Tools::CodonOptTable->new(-file => "contig.fasta",
  
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                                              -genetic_code => 1,                                              -genetic_code => 1,
                                              );                                              );
-B<#If you have Accession number and want to get file from NCBI> my $seqobj = Bio::Tools::CodonOptTable->new(-ncbi_id => "J00522",+</code> 
 +B<#If you have Accession number and want to get file from NCBI> <code>my $seqobj = Bio::Tools::CodonOptTable->new(-ncbi_id => "J00522",
  
 -genetic_code => 1,); -genetic_code => 1,);
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         }         }
         }         }
-B<# To get the prefered codon list based on RSCU & RAC Values > my $prefered_codons = $seqobj->prefered_codon($myCodons);+</code> 
 +B<# To get the prefered codon list based on RSCU & RAC Values ><code> my $prefered_codons = $seqobj->prefered_codon($myCodons);
  
 while ( my ($amino_acid, $codon) = each(%$prefered_codons) ) { while ( my ($amino_acid, $codon) = each(%$prefered_codons) ) {
  
 print "AminoAcid : $amino_acid \t Codon : $codon\n"; } print "AminoAcid : $amino_acid \t Codon : $codon\n"; }
 +</code>
 B<# To produce a graph between RSCU & RAC> # Graph output file extension should be GIF, we support GIF only B<# To produce a graph between RSCU & RAC> # Graph output file extension should be GIF, we support GIF only
- +<code> 
-$seqobj->generate_graph($myCodons,"myoutput.gif");+$seqobj->generate_graph($myCodons,"myoutput.gif");</code>
bio/tools/codonopttable.txt · Last modified: 2010/06/30 19:52 by 172.26.15.75