Permalink
Switch branches/tags
tag-ensembl-stable-061 start snapshot-at-head-of-07-branch release-ensembl-06 release-06 release-06-2 release-1_01 release-1-7-1 release-1-7-0 release-1-7-0-RC6 release-1-7-0-RC5 release-1-7-0-RC4 release-1-6-zenodo release-1-6-924 release-1-6-923 release-1-6-922 release-1-6-921 release-1-6-920 release-1-6-910 release-0-9-3 release-0-9-2 release-0-9-0 release-0-7-2 release-0-7-1 release-0-7-0 release-0-05 release-0-05-1 release-0-04-4 release-0-04-3 release-0-04-2 release-0-04-1 prerelease-06 ontology-overhaul-start ontology-overhaul-end ontology-fix1 lightweight_feature join-0-04-to-0-05 gbrowse_1_65 for_gmod_0_003 bioperl-run-release-1-2-0 bioperl-release-1-6 bioperl-release-1-6-901 bioperl-release-1-6-9 bioperl-release-1-6-1 bioperl-release-1-5-2 bioperl-release-1-5-2-patch2 bioperl-release-1-5-2-patch1 bioperl-release-1-5-1 bioperl-release-1-5-1-rc4 bioperl-release-1-5-0 bioperl-release-1-5-0-rc2 bioperl-release-1-5-0-rc1 bioperl-release-1-4-0 bioperl-release-1-2-3 bioperl-release-1-2-2 bioperl-release-1-2-1 bioperl-release-1-2-0 bioperl-release-1-1-0 bioperl-release-1-0-2 bioperl-release-1-0-1 bioperl-release-1-0-0 bioperl-devel-1-3-04 bioperl-devel-1-3-03 bioperl-devel-1-3-02 bioperl-devel-1-3-01 bioperl-devel-1-1-1 bioperl-061-pre1 bioperl-06-1 bioperl-1-6-RC4 bioperl-1-6-RC3_15392 bioperl-1-6-RC3 bioperl-1-6-RC2_15306 bioperl-1-6-RC2 bioperl-1-6-RC1 bioperl-1-6-0_006 bioperl-1-6-0_005 bioperl-1-6-0_004 bioperl-1-6-0_003 bioperl-1-6-0_002 bioperl-1-6-0_001 bioperl-1-2-1-rc1 bioperl-1-0-alpha2-rc bioperl-1-0-alpha bioperl-1-0-0 before-05-to-06-trunk before-05-to-06-merge after004 after-05-06-merge after-05-06-merge-2
Nothing to show
Find file
Fetching contributors…
Cannot retrieve contributors at this time
executable file 59 lines (47 sloc) 1.79 KB
#!/usr/bin/perl
use strict;
use Bio::LiveSeq::IO::BioPerl;
use Bio::LiveSeq::Mutator;
use Bio::LiveSeq::Mutation;
use Bio::Variation::IO;
if ($#ARGV < 1) { # one argument input
print <<USAGE;
LiveSeq::Mutator example by Joseph Insana
Arguments: filename containing embl entry, gene_name
It will create that Bio::LiveSeq::Gene and print out some
basic informations about it.
It will then issue mutations and print results
Usage: change_gene.pl filename genename
Example: change_gene.pl ../../t/data/ar.embl AR
USAGE
exit;
} else {
my $filename=$ARGV[0];
my $loader=Bio::LiveSeq::IO::BioPerl->load(-file => "$filename");
my $gene_name=$ARGV[1];
my $gene=$loader->gene2liveseq(-gene_name => $gene_name,
-getswissprotinfo => 0);
print STDERR "Gene: ",$gene->name,"\n";
print STDERR " Moltype: ", $gene->get_DNA->alphabet, "\n";
print STDERR " Features:\n";
print STDERR $gene->printfeaturesnum();
print STDERR " Gene has boundaries ",$gene->upbound," - ",$gene->downbound,"\n";
print STDERR " Gene has maxtranscript with start ",$gene->maxtranscript->start,
" end ",$gene->maxtranscript->end," strand ",$gene->maxtranscript->strand,"\n";
print STDERR " DNA has boundaries ",$gene->get_DNA->start," - ",$gene->get_DNA->end,"\n";
print STDERR "\n";
print STDERR "Now issuing mutations to the gene....\n";
my $mutation = new Bio::LiveSeq::Mutation (-seq =>'A',
-pos => 64
);
my $mutate = Bio::LiveSeq::Mutator->new(-gene => $gene,
-numbering => "coding"
);
$mutate->add_Mutation($mutation);
my $results=$mutate->change_gene();
print "\n";
if ($results) {
my $out = Bio::Variation::IO->new( '-format' => 'flat');
$out->write($results);
}
}