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BikePower/HTML.pm view on Meta::CPAN
['transeff', 'transmission_efficiency'],
['rollfriction', 'rolling_friction'],
['weightcyclist', 'weight_cyclist'],
['weightmachine', 'weight_machine'],
) {
my($cgidef, $method) = ($_->[0], $_->[1]);
if (exists $bikepower_def{$cgidef}) {
my $eval = '$bp_obj->' . $method . '($bikepower_def{$cgidef})';
eval $eval;
warn $@ if $@; # XXX
}
}
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examples/parse_entrez_gene_example.pl view on Meta::CPAN
}
# tracking info about how this gene has changed
if(safeval($seq, '{track-info}->[0]->{current-id}'))
{
my (@ids, $newegid, $newllid);
foreach my $id (@{$seq->{'track-info'}->[0]->{'current-id'}})
{
my $tmpid = safeval($id, '{tag}->[0]->{id}');
push(@ids, "$id->{db}:$tmpid");
$newegid = $tmpid if($id->{db} =~ /^GeneID$/i);
$newllid = $tmpid if($id->{db} =~ /^LocusID$/i);
}
my $comment = "Gene moved: current IDs are: " . join(' ; ', @ids);
}
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lib/Bio/Affymetrix/CHP.pm view on Meta::CPAN
return $self->{"no_qc_units"};
}
# MS COM prog ID
=head2 original_com_progid
Arg [0] : none
Example : my $com_id=$chp->original_com_progid()
Description: Gets the progid of the original Microsoft COM object that made
this CHP file
Returntype : string
Exceptions : none
Caller : general
=cut
sub original_com_progid {
my $self=shift;
return $self->{"com_progid"};
}
# CEL file name this CHP file originated from
=head2 CEL_file_name
lib/Bio/Affymetrix/CHP.pm view on Meta::CPAN
if ($self->{"chip_type"}!=0) {
croak "This software does not process non-expression arrays";
}
$self->{"com_progid"}=$self->unpack_length_string($fh);
$self->{"cel_file_name"}=$self->unpack_length_string($fh);
$self->{"probe_array_type"}=$self->unpack_length_string($fh);
lib/Bio/Affymetrix/CHP.pm view on Meta::CPAN
if ($self->{"probe_array_type"} ne $self->{"cdf"}->name()) {
carp "The CDF object you have supplied does not have the same name as the CDF file used to make this CHP file. Results may be dubious";
}
$self->{"com_progid"}=$self->unpack_length_string($fh);
# Actual data. This is the bit that would need to be added to, if we did SNP etc. arrays
{
my %data;
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test-files/test-bioseq.gb view on Meta::CPAN
VRKGPVFSNVILADEINRAPAKVQSALLEAMGERQVTLGDETHRLPDPFFVLATQNPI
EQEGTYNLPESQLDRFLLKVNVHYPSVQDEVRLLKIFSVDGRLENIKVAKVMNAYSLA
DIKRTVGRVKVDDKIMLYIVTLISASRERDKKTYPFAKYIEFGASPRASLSLLKCARV
NALYEGRIFVLPEDVKAVAYSVLRHRITPSYEAEVEEMSIDDIIRMLLSAVALP"
gene complement(178917..179543)
/gene="gidB"
/locus_tag="BB_0177"
CDS complement(178917..179543)
/gene="gidB"
/locus_tag="BB_0177"
/EC_number="2.1.-.-"
/note="identified by match to protein family HMM PF02527;
match to protein family HMM TIGR00138"
/codon_start=1
test-files/test-bioseq.gb view on Meta::CPAN
/translation="MISDIEFALSEHNFQFAYKDLQKINLYIKRILLLNTRFNLISNS
NSNFNSILNLHVIDSLLGLSTVKEINPSEVLDVGSGAGFPGIILAIFDSSRKYYLLER
SKKKSTFLKMIKLELDLENVKILEYEIEKEKKKYEFITIRAFRNMNEYALILKNLLKG
GGLIMAYKGKFDRINLEVNQIKNLFSKIEVKSLNSKLRVDRNLVLLYR"
gene complement(179540..181405)
/gene="gidA"
/locus_tag="BB_0178"
CDS complement(179540..181405)
/gene="gidA"
/locus_tag="BB_0178"
/note="identified by match to protein family HMM PF01134;
match to protein family HMM TIGR00136"
/codon_start=1
/transl_table=11
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bin/BS_CodonJuggler.pl view on Meta::CPAN
#Do reporting
print "\nReport:\n";
foreach my $gname (sort keys %{$state})
{
my $gid = $state->{$gname}->[3];
my @results = @{$state->{$gname}};
next unless($results[0] || $results[1] || $results[2]);
print $gname, q{ : };
if ($results[0])
{
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bin/cx-enscore2chaos.pl view on Meta::CPAN
my $cdsseq = '';
my $in_cds = 0;
foreach my $exon (@exons) {
my ($min, $max, $strand, $contig_id) =
$exon->getl(qw(contig_start contig_end contig_strand contig_id));
my $ctgid = $exon->sget_contig_id."-ct";
my ($nb, $ne) = bcmm2ibv($min, $max, $strand);
my $contig = $contigh{$contig_id};
my $dna = $contig->sget("dna/sequence");
my $exonseq = cutseq($dna, $nb, $ne);
$mrnaseq .= $exonseq;
bin/cx-enscore2chaos.pl view on Meta::CPAN
cutseq($exonseq,
$tnrelpos,
length($exonseq),
1);
$tnfloc->set_nbeg($nb + $tnrelpos * $strand);
$tnfloc->set_srcfeature_id($ctgid);
if ($exon->sget_exon_id eq
$translation->sget_end_exon_id) {
$tnfloc->set_nend($nb +
$translation->sget_seq_end * $strand);
bin/cx-enscore2chaos.pl view on Meta::CPAN
cutseq($exonseq,
0,
$tnrelpos,
1);
$tnfloc->set_nend($nb + $tnrelpos * $strand);
if ($ctgid ne $tnfloc->sget_srcfeature_id) {
$tnC->add_featureprop(N(featureprop=>[type=>"problem",
value=>"CDS range split across contigs; also on $ctgid"]));
}
}
else {
# continuation of CDS
$cdsseq .= $exonseq if $in_cds;
bin/cx-enscore2chaos.pl view on Meta::CPAN
type=>'exon',
featureloc=>[
nbeg=>$nb,
nend=>$ne,
strand=>$strand,
srcfeature_id=>$ctgid,
]
]);
push(@exC, $f);
push(@F, $f);
push(@F,
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lib/Bio/Cluster/UniGene.pm view on Meta::CPAN
sub new {
# standard new call..
my($caller,@args) = @_;
my $self = $caller->SUPER::new(@args);
my ($ugid,$desc,$mems,$size,$species,$dispid,$id,$ns,$auth,$v,$seqfact) =
$self->_rearrange([qw(UNIGENE_ID
DESCRIPTION
MEMBERS
SIZE
SPECIES
lib/Bio/Cluster/UniGene.pm view on Meta::CPAN
SEQFACTORY
)], @args);
$self->{'_alphabet'} = 'dna';
$self->unigene_id($ugid) if $ugid;
$self->description($desc) if $desc;
$self->sequences($mems) if $mems;
$self->size($size) if defined($size);
$self->display_id($dispid) if $dispid; # overwrites ugid
$self->object_id($id) if $id; # overwrites dispid
$self->namespace($ns || 'UniGene');
$self->authority($auth || 'NCBI');
$self->version($v) if defined($v);
if( ! defined $seqfact ) {
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lib/Bio/DB/GFF.pm view on Meta::CPAN
$self->_feature_by_id($id,'feature',$callback);
return wantarray ? @$features : $features->[0];
}
*fetch_feature_by_id = \&get_feature_by_id;
=head2 get_feature_by_gid
Title : get_feature_by_gid
Usage : $db->get_feature_by_gid($id)
Function: fetch segments by feature ID
Returns : a Bio::DB::GFF::Feature object
Args : the feature ID
Status : public
lib/Bio/DB/GFF.pm view on Meta::CPAN
The group ID is often more interesting than the feature ID, since
groups can be complex objects containing subobjects.
=cut
sub get_feature_by_gid {
my $self = shift;
my $id = ref($_[0]) eq 'ARRAY' ? $_[0] : \@_;
my %groups; # cache the groups we create to avoid consuming too much unecessary memory
my $features = [];
my $callback = sub { push @$features,$self->make_feature(undef,\%groups,@_) };
$self->_feature_by_id($id,'group',$callback);
return wantarray ? @$features : $features->[0];
}
*fetch_feature_by_gid = \&get_feature_by_gid;
=head2 delete_fattribute_to_features
Title : delete_fattribute_to_features
Usage : $db->delete_fattribute_to_features(@ids_or_features)
lib/Bio/DB/GFF.pm view on Meta::CPAN
my $next = shift @{$self->{ids}};
return unless $next;
my $name = ref($next) eq 'ARRAY' ? Bio::DB::GFF::Featname->new(@$next) : $next;
my $segment = $self->{type} eq 'name' ? $self->{db}->segment($name)
: $self->{type} eq 'feature' ? $self->{db}->fetch_feature_by_id($name)
: $self->{type} eq 'group' ? $self->{db}->fetch_feature_by_gid($name)
: $self->throw("Bio::DB::GFF::ID_Iterator called to fetch an unknown type of identifier");
$self->throw("id does not exist") unless $segment;
return $segment;
}
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lib/Bio/DB/EntrezGene.pm view on Meta::CPAN
Args : %qualifiers = a hash of qualifiers (ids, format, etc)
=head2 get_Stream_by_id
Title : get_Stream_by_id
Usage : $stream = $db->get_Stream_by_id( [$gid1, $gid2] );
Function: Gets a series of Seq objects using Gene ids
Returns : A Bio::SeqIO stream object
Args : A reference to an array of Gene ids
=head2 request_format
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lib/Bio/DB/SeqFeature/Store/DBI/MariaDB.pm view on Meta::CPAN
my $attribute = $self->_attribute_table;
$self->_delete_index($attribute,$id);
my $sth = $self->_prepare("INSERT INTO $attribute (id,attribute_id,attribute_value) VALUES (?,?,?)");
for my $tag ($obj->get_all_tags) {
my $tagid = $self->_attributeid($tag);
for my $value ($obj->get_tag_values($tag)) {
$sth->execute($id,$tagid,$value) or $self->throw($sth->errstr);
}
}
$sth->finish;
}
lib/Bio/DB/SeqFeature/Store/DBI/MariaDB.pm view on Meta::CPAN
my $self = shift;
my ($obj,$id) = @_;
my $fh = $self->dump_filehandle('attribute');
my $dbh = $self->dbh;
for my $tag ($obj->all_tags) {
my $tagid = $self->_attributeid($tag);
for my $value ($obj->each_tag_value($tag)) {
print $fh join("\t",$id,$tagid,$dbh->quote($value)),"\n";
}
}
}
sub coverage_array {
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t/data/taxdump/names.dmp view on Meta::CPAN
9443 | Primata | | synonym |
9443 | Primates | | scientific name |
9443 | primate | | equivalent name |
9526 | Catarrhini | | scientific name |
9604 | Hominidae | | scientific name |
9604 | Pongidae | | synonym |
27591 | Gazella granti | | scientific name |
27591 | Grant's gazelle | | genbank common name |
27592 | Bovinae | | scientific name |
27596 | Anoa depressicornis | | synonym |
27596 | Bubalis depressicornis | | misspelling |
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t/data/names.dmp view on Meta::CPAN
9443 | Primata | | synonym |
9443 | Primates | | scientific name |
9443 | primate | | equivalent name |
9526 | Catarrhini | | scientific name |
9604 | Hominidae | | scientific name |
9604 | Pongidae | | synonym |
27591 | Gazella granti | | scientific name |
27591 | Grant's gazelle | | genbank common name |
27592 | Bovinae | | scientific name |
27596 | Anoa depressicornis | | synonym |
27596 | Bubalis depressicornis | | misspelling |
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lib/Bio/DOOP/SequenceFeature.pm view on Meta::CPAN
sub get_tfbsid {
my $self = shift;
return($self->{TFBSID});
}
=head2 get_cpgid
Returns the cpg primary ID, if the feature type is "cpg".
=cut
sub get_cpgid {
my $self = shift;
return($self->{CPGID});
}
=head2 get_repeatid
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lib/Bio/Das/ProServer/SourceAdaptor.pm view on Meta::CPAN
#########
# Now add the "residues" to the chain
#
for my $group (@{$chain->{'groups'}}) {
my $gid = $group->{'id'};
my $icode = $group->{'icode'} || q();
#########
# Residue properties
#
$response .= sprintf q(<group type="%s" groupID="%s" name="%s" %s>),
$group->{'type'},
$gid,
$group->{'name'},
$icode ? qq(insertCode="$icode") : q();
#########
# Add the atoms to the chain
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lib/Bio/EnsEMBL/Map/DBSQL/DitagAdaptor.pm view on Meta::CPAN
Caller : general
=cut
sub fetch_by_dbID {
my ($self, $tagid) = @_;
if(!$tagid){
throw "must be called with the type of a ditag.";
}
my $sth = $self->prepare("SELECT d.ditag_id, d.name, d.type, d.tag_count, d.sequence
FROM ditag d
WHERE d.ditag_id = ?");
$sth->execute($tagid);
my $result = $self->_fetch($sth);
return $result->[0];
}
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install_util/cgi_install.PLS view on Meta::CPAN
if (! (-e $cgi_target) ) {
mkpath($cgi_target,0,0777) or die "unable to create $cgi_target directory\n";
}
my $cgidir = "cgi-bin";
chdir $cgidir;
foreach (glob('*')) {
next if /README/;
next if /Makefile/;
next if /CVS/;
next if /^[.\#]/;
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data/controlled_vocab/AL_Medium.xml view on Meta::CPAN
<?xml version="1.0" standalone="yes"?>
<controlled_vocabulary db_table="ArrayLayout" db_column="medium" cv_table="AL_Medium">
<comment type="definition">Referred to in the Array Layout Spots table and used to describe the medium on which the the probe is deposited
</comment>
<term name="glass_slide"
description="user sequence features are spotted on a rigid silicon-based support medium"/>
<term name="nylon_membrane"
description="user sequence features are spotted on a nylon-coated flexible medium"/>
<term name="nitrocellulose"
description="user sequence features are spotted on a nitrocellulose medium"/>
<term name="gel_sieve"
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lib/Bio/Gonzales/Domain/Group.pm view on Meta::CPAN
my ( $self, $dest ) = @_;
my $hits = $self->filter_hits;
my $gffout = Bio::Gonzales::Feat::IO::GFF3->new( file_or_fh => $dest, mode => '>' );
my $gidcs = $self->group_idcs;
while ( my ( $d, $idx ) = each %$gidcs ) {
$gffout->write_comment(" Group $idx contains domain: $d");
}
my $i = 0;
for my $max (@$hits) {
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lib/Bio/Homology/InterologWalk.pm view on Meta::CPAN
@genes = @{$source_species_gene_adaptor->fetch_all_by_external_name($ID)};
}
foreach my $gene (@genes){
my $all_homologies;
my $gid = $gene->stable_id;
my $member = $member_adaptor->fetch_by_source_stable_id("ENSEMBLGENE", $gid);
if (defined $member){
if($destorg eq "All"){ #all destination genomes
$all_homologies = $homology_adaptor->fetch_all_by_Member($member);
}else{ #one destination genome
$all_homologies = $homology_adaptor->fetch_all_by_Member_MethodLinkSpeciesSet($member, $orthologues_mlss);
}
}else{
print "$gid ..no member object defined in Ensembl, skipping..\n";
next;
}
next if (scalar(@$all_homologies) == 0);
print $gid, " ", ($gene->external_name || '-'), "\t";
$counter = _process_homologies(homology_query_id => $gid,
homology_vector => $all_homologies,
protein_adaptor => $proteintree_adaptor,
outfile => $out_data,
hq_only => $onetoone_only
);
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lib/Bio/KBase/InvocationService/InvocationServiceImpl.pm view on Meta::CPAN
my @files;
my $dh;
opendir($dh, $dir) or die "Cannot open directory: $!";
while (my $file = readdir($dh)) {
next if ($file =~ m/^\./);
my($dev, $ino, $mode, $nlink, $uid, $gid, $rdev, $size, $atime, $mtime, $ctime, $blksize, $blocks) = stat("$dir/$file");
my $date= strftime("%b %d %G %H:%M:%S", localtime($mtime));
if (-f "$dir/$file") {
push @files, { name => $file, full_path => "$fpath/$file", mod_date => $date, size => $size};
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mcprimers.pl view on Meta::CPAN
####################################################################
sub sanity_check_arguments {
(my $dev,my $ino,my $mode,my $nlink,my $uid,my $gid,my $rdev,my $size,
my $atime,my $mtime,my $ctime,my $blksize,my $blocks)
= stat(*STDIN);
if ($flag{filter} == 0 and $size > 0) {
die "\nError - Input is redirected and -filter flag not set\n\n";
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lib/Bio/MUST/Apps/FortyTwo/Manual.pod view on Meta::CPAN
# Genus species_taxonid@protacc
>Arabidopsis thaliana_3702@AAO44026
# Genus species_subspecies_taxonid@protacc
>Arabidopsis lyrata_lyrata_81972@EFH60692
# Genus species_taxonid@protacc
>Archaeoglobus fulgidus_2234@WP_048095550
# Genus species_strain_taxonid@protacc
>Archaeoglobus fulgidus_DSM4304_224325@AAB90113
# Genus species_strain_taxonid@protacc
>archaeon 13_1_20CM_2_54_9_1805008@OLE74253
=head3 Reference organisms (C<ref_orgs>, C<ref_banks>)
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test/seq_in1.fasta view on Meta::CPAN
EALEGADMVFVTCGLGGGTGTGAAPVIAEMAKKMGALTVSVVTLPFTMEGIRRAKNAEYG
LKRLAKASDTVIVIPNDKLLEVAPKLPIQMAFKVADEILVQAVKGITELITKPGLVNLDF
NDVRAVMKDGGVAMIGIGESDSEKRALEAAEQALNSPLLDVDISGAKGALISISGADVKL
EEAQQIIEYVTRNVDPKAQVIWGIQLEPELEKTIRVMVIVTGVTSRYITFQEETPEPSEE
EVPPVKIDIPEL
>sp|O29715|FTSZ1_ARCFU Cell division protein FtsZ 1 OS=Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) GN=ftsZ1 PE=3 SV=1
MFMKSIVEEALARAEREKKERIEGRGFEDVEDEILQVLHELKTVIKVIGVGGGGCNTITR
MYEEGIEGAELIALNTDVQHLYYTKANRRILIGKRRTRGLGAGSLPQVGEEAARESEDEI
KKLVEGSDMVFVTCGLGGGTGTGAAPVVAEAAQEAGALTIAVVTFPFSAEGAVRRANAEA
GLERLREVADTVIVIPNDRLLEVVPNYPMQLAFKVADEILMRAVKGITELITKPALINLD
FADVRTVMEKGGVAMIGLGEASGEDKAAESVRKALKSPLLDVDVSGAKAALVNVTGGPDM
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lib/Bio/MUST/Core/Roles/Listable.pm view on Meta::CPAN
# #File c111_78.nbs created on Tuesday 5 May 2009 at 11 hours 40
# #184 positions remain on the 184 aligned positions
# #life.col,life.nom
# #Here is the list of the 78 species used:
# Aciduliprofundum_boonei_T469___________________________________________________ Aeropyrum_pernix_K1____________________________________________________________
# Archaeoglobus_fulgidus_DSM_4304________________________________________________ Archaeoglobus_profundus_Av18__DSM_5631_________________________________________
# ...
my @ids = $self->all_seq_ids;
open my $out, '>', $outfile;
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test/fragmentsseq_profile_out.fasta view on Meta::CPAN
---EQA-----------------LNS-----PL--------LDV-------DISGAKGAL
ISISG-AD----V----KLEEAQQIIE------------YVTRNVD--------PKAQ--
------VIWGIQ--LEPELE-KTIRVMVIVTGV-T-SRY----------------ITFQE
-ET---PEP------------------SEEEVPPVK----------------ID-I----
-PEL--------------------------
>sp|O29715|FTSZ1_ARCFU Cell division protein FtsZ 1 OS=Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) GN=ftsZ1 PE=3 SV=1
MFMKSIVEEALA----RAEREK------------------KERIEG---RGFEDVEDEIL
QVLHELKTVIKVIGVGGGGCNTIT------RM--YE----------EG-------IE---
G---AEL---------------I--ALNT---DVQHLYYTK---ANRRILIGKRRTRGLG
AGSLPQVGEEAARESEDEIKK-----LV------EG-----S---DMVFVTCGLGGGTGT
GAAPVVAE--AAQE---A--GALTI-AVV-TFPFSAEGAVRRANAEAGLERLREV-ADTV
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lib/Bio/MaxQuant/Evidence/Statistics.pm view on Meta::CPAN
my $result = {};
foreach my $experiment(keys %$data){
if(! exists $opts{experiment} || $experiment =~ /$opts{experiment}/){
$result->{$experiment} = {};
my $exptdata = $data->{$experiment};
foreach my $pgid(keys %$exptdata){
if(! exists $opts{proteinGroupId} || $pgid =~ /$opts{proteinGroupId}/){
my $pgdata = $exptdata->{$pgid};
if(! exists $opts{leadingProteins} || $pgdata->{'Leading Proteins'} =~ /$opts{leadingProteins}/){
if(! exists $opts{notLeadingProteins} || $pgdata->{'Leading Proteins'} !~ /$opts{notLeadingProteins}/){
$result->{$experiment}->{$pgid} = $pgdata;
}
}
}
}
}
lib/Bio/MaxQuant/Evidence/Statistics.pm view on Meta::CPAN
my ($o, %opts) = @_; # can set filter here
$o->logRatios();
foreach my $replicate($o->experiments()){
my $median = $o->replicateMedian(%opts, experiment=>$replicate);
my $p = $o->filter(experiment=>$replicate);
foreach my $pgid(keys %{$p->{data}->{$replicate}}){
foreach my $i(0.. $#{$p->{data}->{$replicate}->{$pgid}->{'Ratio H/L'}}){
if($p->{data}->{$replicate}->{$pgid}->{'Ratio H/L'}->[$i] =~ /\d/){
$p->{data}->{$replicate}->{$pgid}->{'Ratio H/L'}->[$i] -= $median;
}
}
}
}
# i guess we should do something better with generating this status:
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lib/Bio/NEXUS/Util/Exceptions.pm view on Meta::CPAN
'trace' => Bio::NEXUS::Util::StackTrace->new,
'time' => CORE::time(),
'pid' => $$,
'uid' => $<,
'euid' => $>,
'gid' => $(,
'egid' => $),
};
return bless $self, $class;
}
sub as_string {
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lib/Bio/PDB/Structure.pm view on Meta::CPAN
Return an atom object that sits at the center of mass for the given molecule.
=item * $object->translate(x,y,z)
Translate the molecule as a rigid object by x,y,z.
=item * $object->rotate(u11,u12,u13,u21,u22,u23,u31,u32,u33)
Do a rigid rotation of the molecule using matrix u.
=item * $object->rotate_translate(@matrix,@vector)
Apply a rotation matrix followed by a translation. To facilitate structural