BioPerl

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Bio/DB/GFF.pm  view on Meta::CPAN

=head2 lock_on_load

 Title   : lock_on_load
 Usage   : $lock = $db->lock_on_load([$lock])
 Function: set write locking during load
 Returns : current value of lock-on-load flag
 Args    : new value of lock-on-load-flag
 Status  : Public

This method is honored by some of the adaptors.  If the value is true,
the tables used by the GFF modules will be locked for writing during
loads and inaccessible to other processes.

=cut

sub lock_on_load {
  my $self = shift;
  my $d = $self->{lock};
  $self->{lock} = shift if @_;
  $d;
}

Bio/Root/Utilities.pm  view on Meta::CPAN

#-------------
    my( $self, @param) = @_;
    my($recipient,$subj,$message,$cc) = $self->_rearrange([qw(TO SUBJ MSG CC)],@param);

    $self->throw("Invalid or missing e-mail address: $recipient")
        if not $recipient =~ /\S+\@\S+/;

    $subj ||= 'empty subject'; $message ||= '';

    # Best to use mail rather than sendmail. Permissions on sendmail in
    # linux distros have been significantly locked down in recent years,
    # due to the perception that it is insecure.
    my ($exe, $ccinfo);
    if ($exe = $self->find_exe('mail')) {
        if (defined $cc) {
            $ccinfo = "-c $cc";
        }
        $self->debug("send_mail: $exe -s '$subj' $ccinfo $recipient\n");
        open (MAIL, "| $exe -s '$subj' $ccinfo $recipient") ||
            $self->throw("Can't send email: mail cannot fork: $!");
        print MAIL <<QQ_EOFM_QQ;

examples/tk/gsequence.pl  view on Meta::CPAN

my ($dblink_window,@dblink_entry,$current_dblink,$dblink_clist,$dblink_handler_id);
my ($ref_window,@ref_entry,$current_ref,$ref_clist,$ref_handler_id);
my ($feature_window,@feature_entry,$current_feature_item,@feature_spinner,
    $feature_handler_id,$feature_tree);
my ($pref_window,@pref_entry);

# global file data
my @seq;
my @filename;
my @modified;
my @locked; # locked sequence for editing ?
my $current;

# menu
my @menu_items = ( { path        => '/_File',
		     type        => '<Branch>' },
		   { path        => '/File/_New',
		     accelerator => '<control>N',
		     callback    => \&new },
		   { path        => '/File/_Open SwissProt',
		     accelerator => '<control>O',

t/data/NC_000007-ribosomal-slippage.gb  view on Meta::CPAN

                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /db_xref="GeneID:10282"
                     /db_xref="HGNC:14562"
                     /db_xref="HPRD:16107"
                     /db_xref="MIM:605456"
     mRNA            complement(join(93621000..93623697,93625577..93625633,
                     93628482..93628606,93633510..93633690))
                     /gene="BET1"
                     /gene_synonym="DKFZp781C0425; HBET1"
                     /product="blocked early in transport 1 homolog (S.
                     cerevisiae)"
                     /note="Derived by automated computational analysis using
                     gene prediction method: BestRefseq."
                     /transcript_id="NM_005868.4"
                     /db_xref="GI:83779007"
                     /db_xref="GeneID:10282"
                     /db_xref="HGNC:14562"
                     /db_xref="HPRD:16107"
                     /db_xref="MIM:605456"
     CDS             complement(join(93623542..93623697,93625577..93625633,

t/data/consed_project/edit_dir/test_project.phrap.out  view on Meta::CPAN

         0      2      3      4      5    Total
0        0      1      7      7      8       23
2        1      0      0      0      0        1
3        7      0      0      0      0        7
4        7      0      0      0      0        7
5        8      0      0      0      0        8

Histogram of spacings between adjacent indel pairs:


Blocked reads: 
ML4924F 11 600  left 
ML4924R 56 753  left 

2 blocked reads: 2 left only, 0 right only, 0 both.
0 reads (not shown) lack a high-quality segment.

0 perfect duplicates

2 isolated singlets (having no non-vector match to any other read): 
  Read         Length      (# trimmed non-X bases)
 ML4922R        753   (668)
 ML4947F        739   (658)

Contig 1.  2 reads; 708 bp (untrimmed), 704 (trimmed).  Isolated contig.

t/data/so.obo  view on Meta::CPAN

[Term]
id: SO:0000717
name: reading_frame
def: "A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It does not contain the start or stop codon." [SO:rb]
comment: This term was added after a request by SGD.nAgust 2004. Modified after SO meeting in Cambridge to not include start or stop.
subset: SOFA
is_a: SO:0000001 ! region

[Term]
id: SO:0000718
name: blocked_reading_frame
def: "A reading_frame that is interupted by one or more stop codons; usually identified through intergenomic sequence comparisons." [SO:rb]
comment: Term requested by Rama from SGD
is_a: SO:0000717 ! reading_frame

[Term]
id: SO:0000719
name: ultracontig
def: "An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic...
subset: SOFA
is_a: SO:0000353 ! assembly