use Bio::Seq;
my $seqobj = Bio::Seq->new(
-seq => "ACTGTGTGTCC",
-id => "Chlorella sorokiniana",
-accession_number => "CAA41635"
);
Bio::Seq=HASH(0x7f8d1400a738)
use Data::Dumper;
Dumper($seqobj);
$VAR1 = bless( { 'primary_seq' => bless( { 'length' => 11, 'display_id' => 'Chlorella sorokiniana', 'accession_number' => 'CAA41635', '_root_verbose' => 0, 'seq' => 'ACTGTGTGTCC', '_nowarnonempty' => undef, 'alphabet' => 'dna' }, 'Bio::PrimarySeq' ), '_root_verbose' => 0 }, 'Bio::Seq' );
$seqobj->seq();
ACTGTGTGTCC
$seqobj->subseq(5,10);
TGTGTC
$seqobj->accession_number();
CAA41635
$seqobj->alphabet();
dna
$seqobj->version();
$seqobj->length();
11
$seqobj->desc();
$seqobj->primary_id();
Bio::PrimarySeq=HASH(0x7f8d10eb9e20)
$seqobj->display_id();
Chlorella sorokiniana
$trunc_seq_obj = $seqobj->trunc(5,10);
Bio::Seq=HASH(0x7f8d1400ab88)
print $seqobj->seq(),"\n";
print $trunc_seq_obj->seq(),"\n";
ACTGTGTGTCC TGTGTC
1
$revcom_seq_obj=$seqobj->revcom;
Bio::Seq=HASH(0x7f8d12654130)
print $seqobj->seq(),"\n";
print $revcom_seq_obj->seq(),"\n";
ACTGTGTGTCC GGACACACAGT
1
$translated_seq_obj=$seqobj->translate;
Bio::Seq=HASH(0x7f8d1400ab28)
print $seqobj->seq(),"\n";
print $translated_seq_obj->seq(),"\n";
ACTGTGTGTCC TVC
1
$string = "ATTGCTTT";
print $seqobj->validate_seq($string),"\n";
1
1
$string = "TTT53FFF";
print $seqobj->validate_seq($string),"\n";
0
1
$seq = $seqobj->seq();
print "$seq\n";
ACTGTGTGTCC
1
$length = $seqobj->length();
print "$length\n";
11
1
$subseq = $seqobj->subseq(int($length/2), $length);
print "$subseq\n";
TGTGTCC
1
$new_seq = $seq.$subseq;
if($seqobj->validate_seq($new_seq)){
$seqobj->seq($new_seq);
}
print $seqobj->seq()," ", $seqobj->length(), "\n"
ACTGTGTGTCCTGTGTCC 18
1
$translated_obj = $seq;
if( $seqobj->alphabet() == 'dna'){
$translated_obj = $seqobj->translate();
}
print $translated_obj->seq(),"\n";
TVCPVS
1
use Bio::Tools::SeqStats;
$seq_stats = Bio::Tools::SeqStats->new(-seq => $seqobj);
Bio::Tools::SeqStats=HASH(0x7f8d15079050)
$hash_ref = $seq_stats->count_monomers();
Dumper($hash_ref);
$VAR1 = { 'A' => 1, 'T' => 4, 'C' => 3, 'G' => 3 };
$hash_ref = Bio::Tools::SeqStats->count_codons($seqobj);
Dumper($hash_ref);
$VAR1 = { 'ACT' => 1, 'GTG' => 1, 'TGT' => 1 };
$weight = Bio::Tools::SeqStats->get_mol_wt($seqobj);
Dumper($weight);
$VAR1 = [ '3403.5', '3403.5' ];
Bio::Tools::SeqStats->hydropathicity($seqobj);
------------- EXCEPTION ------------- MSG: hydropathicity only meaningful for protein, not for dna sequences. STACK Bio::Tools::SeqStats::hydropathicity /Users/bbatut/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/Bio/Tools/SeqStats.pm:745 STACK Eval::Closure::Sandbox_627::__ANON__ reply input:1 STACK Reply::Plugin::Defaults::execute /Users/bbatut/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/Reply/Plugin/Defaults.pm:72 STACK Reply::_wrapped_plugin /Users/bbatut/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/Reply.pm:219 STACK Reply::__ANON__ /Users/bbatut/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/Reply.pm:217 STACK Reply::Plugin::IPerl::__ANON__ /Users/bbatut/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/Reply/Plugin/IPerl.pm:28 STACK (eval) /Users/bbatut/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/Capture/Tiny.pm:369 STACK Capture::Tiny::_capture_tee /Users/bbatut/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/Capture/Tiny.pm:369 STACK Reply::Plugin::IPerl::execute /Users/bbatut/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/Reply/Plugin/IPerl.pm:29 STACK Reply::_wrapped_plugin /Users/bbatut/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/Reply.pm:219 STACK Reply::_eval /Users/bbatut/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/Reply.pm:176 STACK Reply::try {...} /Users/bbatut/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/Reply.pm:68 STACK (eval) /Users/bbatut/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/Try/Tiny.pm:81 STACK Try::Tiny::try /Users/bbatut/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/Try/Tiny.pm:72 STACK Reply::step /Users/bbatut/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/Reply.pm:73 STACK Devel::IPerl::Kernel::Backend::Reply::__ANON__ /Users/bbatut/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/Devel/IPerl/Kernel/Backend/Reply.pm:48 STACK (eval) /Users/bbatut/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/Capture/Tiny.pm:369 STACK Capture::Tiny::_capture_tee /Users/bbatut/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/Capture/Tiny.pm:369 STACK Devel::IPerl::Kernel::Backend::Reply::run_line /Users/bbatut/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/Devel/IPerl/Kernel/Backend/Reply.pm:49 STACK Devel::IPerl::Kernel::Callback::REPL::execute /Users/bbatut/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/Devel/IPerl/Kernel/Callback/REPL.pm:42 STACK Devel::IPerl::Kernel::Callback::REPL::execute (eval 55):6 STACK Devel::IPerl::Kernel::Callback::REPL::msg_execute_request /Users/bbatut/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/Devel/IPerl/Kernel/Callback/REPL.pm:155 STACK Devel::IPerl::Kernel::route_message /Users/bbatut/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/Devel/IPerl/Kernel.pm:223 STACK Devel::IPerl::Kernel::__ANON__ /Users/bbatut/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/Devel/IPerl/Kernel.pm:195 STACK IO::Async::Loop::Poll::post_poll /Users/bbatut/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/IO/Async/Loop/Poll.pm:172 STACK IO::Async::Loop::Poll::loop_once /Users/bbatut/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/IO/Async/Loop/Poll.pm:270 STACK IO::Async::Loop::run /Users/bbatut/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/IO/Async/Loop.pm:524 STACK IO::Async::Loop::loop_forever /Users/bbatut/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/IO/Async/Loop.pm:561 STACK Devel::IPerl::Kernel::run /Users/bbatut/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/Devel/IPerl/Kernel.pm:203 STACK Devel::IPerl::main /Users/bbatut/perl5/perlbrew/perls/perl-5.16.0/lib/site_perl/5.16.0/Devel/IPerl.pm:14 STACK toplevel -e:1 -------------------------------------
use Bio::SeqIO;
my $seqio_obj = Bio::SeqIO->new(-file => '>sequence.fasta',
-format => 'fasta' );
Bio::SeqIO::fasta=HASH(0x7f8d1402ffd8)
Dumper($seqio_obj );
use Bio::SeqIO;
use Bio::Seq;
my $seqio_obj = Bio::SeqIO->new(-file => '>sequence.fasta',
-format => 'fasta' );
my $seqobj = Bio::Seq->new(
-seq => "ACTGTGTGTCC",
-id => "Chlorella sorokiniana"
);
$seqio_obj->write_seq($seqobj);
my $seqobj = Bio::Seq->new(
-seq => "ACTGTGTGTCCTGTGTCC",
-id => "Modified Chlorella sorokiniana"
);
$seqio_obj->write_seq($seqobj);
1
--------------------- WARNING --------------------- MSG: No whitespace allowed in FASTA ID [Chlorella sorokiniana] --------------------------------------------------- --------------------- WARNING --------------------- MSG: No whitespace allowed in FASTA ID [Chlorella sorokiniana] --------------------------------------------------- --------------------- WARNING --------------------- MSG: No whitespace allowed in FASTA ID [Modified Chlorella sorokiniana] --------------------------------------------------- --------------------- WARNING --------------------- MSG: No whitespace allowed in FASTA ID [Modified Chlorella sorokiniana] ---------------------------------------------------
use Bio::SeqIO;
$seqio_obj = Bio::SeqIO->new(-file => "sequence.fasta",
-format => "fasta" );
while ($seq_obj = $seqio_obj->next_seq){
print $seq_obj->seq,"\n";
}
ACTGTGTGTCC ACTGTGTGTCCTGTGTCC
use Bio::DB::GenBank;
$db_obj = Bio::DB::GenBank->new;
Bio::DB::GenBank=HASH(0x7f8d15079998)
Dumper($db_obj);
use Bio::DB::GenBank;
use Bio::Seq;
$db_obj = Bio::DB::GenBank->new;
$seq_obj = $db_obj->get_Seq_by_id(2);
print $seq_obj->display_id(),"\n";
A00002
1
use Bio::DB::GenBank;
use Bio::DB::Query::GenBank;
$query = "Arabidopsis[ORGN] AND topoisomerase[TITL] and 0:3000[SLEN]";
$query_obj = Bio::DB::Query::GenBank->new(-db => 'nucleotide', -query => $query );
$gb_obj = Bio::DB::GenBank->new;
$stream_obj = $gb_obj->get_Stream_by_query($query_obj);
while ($seq_obj = $stream_obj->next_seq) {
print $seq_obj->display_id, "\t", $seq_obj->length, "\n";
}
NM_001203615 2099 NM_001125591 549 NM_128760 2775 NM_120360 1655 NM_001036386 2734 NM_112969 2212 NM_126949 704 ATHTOP2A 410 XM_002881164 2698 AF323679 1373 DQ446392 1152 AY142667 2140 AY133820 2113 AY090993 1830 AY080864 928 AY039947 2493 AY034972 2586 U12285 591 U12284 590 AK221851 1078 AK221766 1452 AK221174 2785 AJ297843 2212 AJ297842 1655 AJ251990 1655 AJ251989 1640 AK175923 2744 AK175789 2744
use Bio::SearchIO;
my $in = new Bio::SearchIO(
-format => "blast",
-file => "files/report.bls");
while(my $result = $in->next_result){
while(my $hit = $result->next_hit){
while(my $hsp = $hit->next_hsp){
print "Query=", $result->query_name,
" Hit=", $hit->name,
" Length=", $hsp->length('total'),
" Percent_id=", $hsp->percent_identity,
"\n";
}
}
}
Query=gi|20521485|dbj|AP004641.2 Hit=gb|443893|124775 Length=52 Percent_id=88.4615384615385