Bio::SeqIO::table(3pm)					User Contributed Perl Documentation				    Bio::SeqIO::table(3pm)

NAME

       Bio::SeqIO::table - sequence input/output stream from a delimited table

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 => 'table');

	 while ( my $seq = $stream->next_seq() ) {
	       # do something with $seq
	 }

DESCRIPTION

       This class transforms records in a table-formatted text file into Bio::Seq objects.

       A table-formatted text file of sequence records for the purposes of this module is defined as a text file with each row corresponding to a
       sequence, and the attributes of the sequence being in different columns. Columns are delimited by a common delimiter, for instance tab or
       comma.

       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.

FEEDBACK

   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

   Support
       Please direct usage questions or support issues to the mailing list:

       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.

   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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Hilmar Lapp
       Email hlapp at gmx.net

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

   new
	Title	: new
	Usage	: $stream = Bio::SeqIO->new(-file => $filename, -format => 'table')
	Function: Returns a new seqstream
	Returns : A Bio::SeqIO stream for a table format
	Args	: Named parameters:

		    -file    name of file to read
		    -fh      filehandle to attach to
		    -comment leading character(s) introducing a comment line
		    -header  the number of header lines to skip; the first
			     non-comment header line will be used to obtain
			     column names; column names will be used as the
			     default tags for attaching annotation.
		    -delim   the delimiter for columns as a regular expression;
			     consecutive occurrences of the delimiter will
			     not be collapsed.
		    -display_id the one-based index of the column containing
			     the display ID of the sequence
		    -accession_number the one-based index of the column
			     containing the accession number of the sequence
		    -seq     the one-based index of the column containing
			     the sequence string of the sequence
		    -species the one-based index of the column containing the
			     species for the sequence record; if not a
			     number, will be used as the static species
			     common to all records
		    -annotation if provided and a scalar (but see below), a
			     flag whether or not all additional columns are
			     to be preserved as annotation, the tags used
			     will either be 'colX' if there is no column
			     header and where X is the one-based column
			     index, and otherwise the column headers will be
			     used as tags;

			     if a reference to an array, or a square
			     bracket-enclosed string of comma-delimited
			     values, only those columns (one-based index)
			     will be preserved as annotation, tags as before;

			     if a reference to a hash, or a curly
			     braces-enclosed string of comma-delimited key
			     and value pairs in alternating order, the keys
			     are one-based column indexes to be preserved,
			     and the values are the tags under which the
			     annotation is to be attached; if not provided or
			     supplied as undef, no additional annotation will
			     be preserved.
		    -colnames a reference to an array of column labels, or a
			     string of comma-delimited labels, denoting the
			     columns to be converted into annotation; this is
			     an alternative to -annotation and will be
			     ignored if -annotation is also supplied with a
			     valid value.
		    -trim    flag determining whether or not all values should
			     be trimmed of leading and trailing white space
			     and double quotes

		  Additional arguments may be used to e.g. set factories and
		  builders involved in the sequence object creation (see the
		  POD of Bio::SeqIO).

   next_seq
	Title	: next_seq
	Usage	: $seq = $stream->next_seq()
	Function: returns the next sequence in the stream
	Returns : Bio::Seq::RichSeq object
	Args	:

   comment_char
	Title	: comment_char
	Usage	: $obj->comment_char($newval)
	Function: Get/set the leading character(s) designating a line as
		  a comment-line.
	Example :
	Returns : value of comment_char (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   header
	Title	: header
	Usage	: $obj->header($newval)
	Function: Get/set the number of header lines to skip before the
		  rows containing actual sequence records.

		  If set to zero or undef, means that there is no header and
		  therefore also no column headers.

	Example :
	Returns : value of header (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   delimiter
	Title	: delimiter
	Usage	: $obj->delimiter($newval)
	Function: Get/set the column delimiter. This will in fact be
		  treated as a regular expression. Consecutive occurrences
		  will not be collapsed to a single one.

	Example :
	Returns : value of delimiter (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   attribute_map
	Title	: attribute_map
	Usage	: $obj->attribute_map($newval)
	Function: Get/set the map of sequence object initialization
		  attributes (keys) to one-based column index.

		  Attributes will usually need to be prefixed by a dash, just
		  as if they were passed to the new() method of the sequence
		  class.

	Example :
	Returns : value of attribute_map (a reference to a hash)
	Args	: on set, new value (a reference to a hash or undef, optional)

   annotation_map
	Title	: annotation_map
	Usage	: $obj->annotation_map($newval)
	Function: Get/set the mapping between one-based column indexes
		  (keys) and annotation tags (values).

		  Note that the map returned by this method may change after
		  the first next_seq() call if the file contains a column
		  header and no annotation keys have been predefined in the
		  map, because upon reading the column header line the tag
		  names will be set automatically.

		  Note also that the map may reference columns that are used
		  as well in the sequence attribute map.

	Example :
	Returns : value of annotation_map (a reference to a hash)
	Args	: on set, new value (a reference to a hash or undef, optional)

   keep_annotation
	Title	: keep_annotation
	Usage	: $obj->keep_annotation($newval)
	Function: Get/set flag whether or not to keep values from
		  additional columns as annotation.

		  Additional columns are all those columns in the input file
		  that aren't referenced in the attribute map.

	Example :
	Returns : value of keep_annotation (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   annotation_columns
	Title	: annotation_columns
	Usage	: $obj->annotation_columns($newval)
	Function: Get/set the names (labels) of the columns to be used for
		  annotation.

		  This is an alternative to using annotation_map. In order to
		  have any effect, it must be set before the first call of
		  next_seq(), and obviously there must be a header line (or
		  row) too giving the column labels.

	Example :
	Returns : value of annotation_columns (a reference to an array)
	Args	: on set, new value (a reference to an array of undef, optional)

   trim_values
	Title	: trim_values
	Usage	: $obj->trim_values($newval)
	Function: Get/set whether or not to trim leading and trailing
		  whitespace off all column values.
	Example :
	Returns : value of trim_values (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

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.

   _attribute_map
	Title	: _attribute_map
	Usage	: $obj->_attribute_map($newval)
	Function: Get only. Same as attribute_map, but zero-based indexes.

		  Note that any changes made to the returned map will change
		  the map used by this instance. You should know what you are
		  doing if you modify the returned value (or if you call this
		  method in the first place).

	Example :
	Returns : value of _attribute_map (a reference to a hash)
	Args	: none

   _annotation_map
	Title	: _annotation_map
	Usage	: $obj->_annotation_map($newval)
	Function: Get only. Same as annotation_map, but with zero-based indexes.

		  Note that any changes made to the returned map will change
		  the map used by this instance. You should know what you are
		  doing if you modify the returned value (or if you call this
		  method in the first place).

	Example :
	Returns : value of _annotation_map (a reference to a hash)
	Args	: none

   _header_skipped
	Title	: _header_skipped
	Usage	: $obj->_header_skipped($newval)
	Function: Get/set the flag whether the header was already
		  read (and skipped) or not.
	Example :
	Returns : value of _header_skipped (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   _next_record
	Title	: _next_record
	Usage	:
	Function: Navigates the underlying file to the next record.

		  For row-based records in delimited text files, this will
		  skip all empty lines and lines with a leading comment
		  character.

		  This method is here is to serve as a hook for other formats
		  that conceptually also represent tables but aren't
		  formatted as row-based text files.

	Example :
	Returns : TRUE if the navigation was successful and FALSE
		  otherwise. Unsuccessful navigation will usually be treated
		  as an end-of-file condition.
	Args	:

   _parse_header
	Title	: _parse_header
	Usage	:
	Function: Parse the table header and navigate past it.

		  This method is called if the number of header rows has been
		  specified equal to or greater than one, and positioned at
		  the first header line (row). By default the first header
		  line (row) is used for setting column names, but additional
		  lines (rows) may be skipped too. Empty lines and comment
		  lines do not count as header lines (rows).

		  This method will call _next_record() to navigate to the
		  next header line (row), if there is more than one header
		  line (row). Upon return, the file is presumed to be
		  positioned at the first record after the header.

		  This method is here is to serve as a hook for other formats
		  that conceptually also represent tables but aren't
		  formatted as row-based text files.

		  Note however that the only methods used to access file
		  content or navigate the position are _get_row_values() and
		  _next_record(), so it should usually suffice to override
		  those.

	Example :
	Returns : TRUE if navigation past the header was successful and FALSE
		  otherwise. Unsuccessful navigation will usually be treated
		  as an end-of-file condition.
	Args	:

   _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.

		  This method is here is to serve as a hook for other formats
		  that conceptually also represent tables but aren't
		  formatted as row-based text files.

	Example :
	Returns : An array of column values for the current row.
	Args	:

perl v5.14.2							    2012-03-02						    Bio::SeqIO::table(3pm)