Bio-ToolBox

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lib/Bio/ToolBox.pm  view on Meta::CPAN

=head2 Methods

=over 4

=item load_file

Open a tab-delimited text file as a L<Bio::ToolBox::Data> object. 
Simply pass the file path as a single argument. It assumes the first 
row is the column headers, and comment lines begin with C<#>. 
Compressed files are transparently handled. See the 
L<Bio::ToolBox::Data> C<new> method for more details or options.

  $Data = Bio::ToolBox->load_file('myfile.txt');

For advanced options, pass key =E<gt> value pairs as arguments as
defined for L<Bio::ToolBox::Data> C<new()>.

=item parse_file

Parse an annotation file, such as BED, GTF, GFF3, UCSC genePred or

lib/Bio/ToolBox.pm  view on Meta::CPAN

=item new_bed

Generate a new, empty L<Bio::ToolBox::Data> table formatted
as a BED format. Pass the number of columns desired (integer
in range 3..12 inclusive). Default is 6 (standard BED format).

  $Data = Bio::ToolBox->new_bed(4);

=item read_file

Open a generic file handle for reading. It transparently handles 
compression as necessary. Returns an L<IO::File> object. Pass the 
file path as an argument. 
    
  $fh = Bio::ToolBox->read_file('mydata.txt.gz');
    
=item write_file

Open a generic file handle for writing. It transparently handles 
compression as necessary based on filename extension or passed 
options. It will use the C<pigz> multi-threaded, external, compression
utility if available. See the C<open_to_write_fh> method in 
<Bio::ToolBox::Data::file> for more information.

  $fh = Bio::ToolBox->write_file('mynewdata.txt.gz');

=item open_database

Open a binary database file, including Bam, bigWig, bigBed, Fasta, 
L<Bio::DB::SeqFeature::Store> SQLite file or named MySQL connection, 
USeq file, or any other supported binary or indexed file formats. 
Database type is transparently and automatically checked by looking for 
common file extensions, if present. See the C<open_db_connection> in 
L<Bio::ToolBox::db_helper> for more information.

  $db = Bio::ToolBox->open_database($database);
    
=back

=head1 REPOSITORY

Source code for the Bio::ToolBox package is maintained at 

lib/Bio/ToolBox/Data.pm  view on Meta::CPAN

name. If successful, it will return the name of the file saved.

=back

=head2 Verifying Datasets

When working with row Features and collecting scores, the dataset 
from which you are collecting must be verified prior to collection. 
This ensures that the proper database adaptor is available and loaded, 
and that the dataset is correctly specified (otherwise nothing would be 
collected). This verification is normally performed transparently when 
you call L<get_score|Bio::ToolBox::Data::Feature/get_score> or 
L<get_position_scores|Bio::ToolBox::Data::Feature/get_position_scores>.
However, datasets may be explicitly verified prior to calling the score 
methods. 

=over 4

=item verify_dataset

 my $dataset = $Data->verify_dataset($dataset, $database);

scripts/manipulate_wig.pl  view on Meta::CPAN

=item --help

Display the POD documentation using perldoc. 

=back

=head1 DESCRIPTION

A program to manipulate the score value of wig files. This will process all 
forms of text based wig files, including fixedStep, variableStep, and bedGraph. 
Files may be gzip compressed. BigWig files are also transparently supported as 
both input and output, provided that the appropriate UCSC utility files are 
available.

B<NOTE:> More than one option may be specified! The options above are the order 
in which the score is manipulated. If they are not in the order you want, you 
may have to pipe to sequential instances. Use 'stdin' and 'stdout' for filenames.

=head1 AUTHOR

 Timothy J. Parnell, PhD