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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

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

[email protected]

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://github.com/bioperl/bioperl-live/issues

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    :