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# BioPerl module for Bio::SeqIO::excel
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Hilmar Lapp <hlapp at gmx.net>
#
#
# (c) Hilmar Lapp, hlapp at gmx.net, 2005.
# (c) GNF, Genomics Institute of the Novartis Research Foundation, 2005.
#
# You may distribute this module under the same terms as perl itself.
# Refer to the Perl Artistic License (see the license accompanying this
# software package, or see http://www.perl.com/language/misc/Artistic.html)
# for the terms under which you may use, modify, and redistribute this module.
#
# THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
# MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
#
# POD documentation - main docs before the code
=head1 NAME
Bio::SeqIO::excel - sequence input/output stream from a
MSExcel-formatted table
=head1 SYNOPSIS
#It is probably best not to use this object directly, but
#rather go through the SeqIO handler system. Go:
$stream = Bio::SeqIO->new(-file => $filename, -format => 'excel');
while ( my $seq = $stream->next_seq() ) {
# do something with $seq
}
=head1 DESCRIPTION
This class transforms records in a MS Excel workbook file into
Bio::Seq objects. It is derived from the table format module and
merely defines additional properties and overrides the way to get data
from the file and advance to the next record.
The module permits specifying which columns hold which type of
annotation. The semantics of certain attributes, if present, are
pre-defined, e.g., accession number and sequence. Additional
attributes may be added to the annotation bundle. See
L<Bio::SeqIO::table> for a complete list of parameters and
capabilities.
You may also specify the worksheet from which to obtain the data, and
after finishing one worksheet you may change the name to keep reading
from another worksheet (in the same file).
This module depends on Spreadsheet::ParseExcel to parse the underlying
Excel file.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via email or the web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Hilmar Lapp
Email hlapp at gmx.net
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::SeqIO::excel;
use strict;
use Bio::SeqIO;
use Spreadsheet::ParseExcel;
#use Spreadsheet::ParseExcel::Workbook;
use base qw(Bio::SeqIO::table);
=head2 new
Title : new
Usage : $stream = Bio::SeqIO->new(-file => $filename, -format => 'excel')
Function: Returns a new seqstream
Returns : A Bio::SeqIO stream for a MS Excel format
Args : Supports the same named parameters as Bio::SeqIO::table,
except -delim, which obviously does not apply to a binary
format. In addition, the following parameters are supported.
-worksheet the name of the worksheet holding the table;
if unspecified the first worksheet will be
used
=cut
sub _initialize {
my($self,@args) = @_;
# chained initialization
$self->SUPER::_initialize(@args);
# our own parameters
my ($worksheet) = $self->_rearrange([qw(WORKSHEET)], @args);
# store options and apply defaults
$self->worksheet($worksheet || 0);
}
=head2 worksheet
Title : worksheet
Usage : $obj->worksheet($newval)
Function: Get/set the name of the worksheet holding the table. The
worksheet name may also be a numeric index.
You may change the value during parsing at any time in
order to start reading from a different worksheet (in the
same file).
Example :
Returns : value of worksheet (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub worksheet{
my $self = shift;
if (@_) {
my $sheetname = shift;
# on set we reset the parser here in order to allow reading
# from multiple worksheets in a row
$self->_worksheet(undef) if defined($sheetname);
return $self->{'worksheet'} = $sheetname;
}
return $self->{'worksheet'};
}
=head2 close
Title : close
Usage :
Function: Close and/or release the resources used by this parser instance.
We override this here in order to free up the worksheet and
other related objects.
Example :
Returns :
Args :
=cut
sub close{
my $self = shift;
$self->_worksheet(undef);
# make sure we chain to the inherited method
$self->SUPER::close(@_);
}
=head1 Internal methods
All methods with a leading underscore are not meant to be part of the
'official' API. They are for use by this module only, consider them
private unless you are a developer trying to modify this module.
=cut
=head2 _worksheet
Title : _worksheet
Usage : $obj->_worksheet($newval)
Function: Get/set the worksheet object to be used for accessing cells.
Example :
Returns : value of _worksheet (a Spreadsheet::ParseExcel::Worksheet object)
Args : on set, new value (a Spreadsheet::ParseExcel::Worksheet
object or undef, optional)
=cut
sub _worksheet{
my $self = shift;
return $self->{'_worksheet'} = shift if @_;
return $self->{'_worksheet'};
}
=head2 _next_record
Title : _next_record
Usage :
Function: Navigates the underlying file to the next record.
We override this here in order to adapt navigation to data
in an Excel worksheet.
Example :
Returns : TRUE if the navigation was successful and FALSE
otherwise. Unsuccessful navigation will usually be treated
as an end-of-file condition.
Args :
=cut
sub _next_record{
my $self = shift;
my $wsheet = $self->_worksheet();
if (! defined($wsheet)) {
# worksheet hasn't been initialized yet, do so now
my $wbook = Spreadsheet::ParseExcel::Workbook->Parse($self->_fh);
$wsheet = $wbook->Worksheet($self->worksheet);
# store the result
$self->_worksheet($wsheet);
# re-initialize the current row
$self->{'_row'} = -1;
}
# we need a valid worksheet to continue
return unless defined($wsheet);
# check whether we are at or beyond the last defined row
my ($minrow, $maxrow) = $wsheet->RowRange();
return if $self->{'_row'} >= $maxrow;
# we don't check for empty rows here as in order to do that we'd
# have to know in which column to look
# so, just advance to the next row
$self->{'_row'}++;
# done
return 1;
}
=head2 _get_row_values
Title : _get_row_values
Usage :
Function: Get the values for the current line (or row) as an array in
the order of columns.
We override this here in order to adapt access to column
values to data contained in an Excel worksheet.
Example :
Returns : An array of column values for the current row.
Args :
=cut
sub _get_row_values{
my $self = shift;
# obtain the range of columns - we use all that are defined
my $wsheet = $self->_worksheet();
my ($colmin,$colmax) = $wsheet->ColRange();
# build the array of columns for the current row
my @cols = ();
my $row = $self->{'_row'};
for (my $i = $colmin; $i <= $colmax; $i++) {
my $cell = $wsheet->Cell($row, $i);
push(@cols, defined($cell) ? $cell->Value : $cell);
}
# done
return @cols;
}
1;
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