NAME
FAST::Bio::LocatableSeq - A FAST::Bio::PrimarySeq object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq.
SYNOPSIS
use FAST::Bio::LocatableSeq;
my $seq = FAST::Bio::LocatableSeq->new(-seq => "CAGT-GGT",
-id => "seq1",
-start => 1,
-end => 7);
# a normal sequence object
$locseq->seq();
$locseq->id();
# has start,end points
$locseq->start();
$locseq->end();
# inherits off RangeI, so range operations possibleDESCRIPTION
The LocatableSeq sequence object was developed mainly because the SimpleAlign object requires this functionality, and in the rewrite of the Sequence object we had to decide what to do with this.
It is, to be honest, not well integrated with the rest of bioperl. For example, the trunc() function does not return a LocatableSeq object, as some might have thought. Also, the sequence is not a FAST::Bio::SeqI, so the location is simply inherited from FAST::Bio::RangeI and is not stored in a FAST::Bio::Location.
There are all sorts of nasty gotcha's about interactions between coordinate systems when these sort of objects are used. Some mapping now occurs to deal with HSP data, however it can probably be integrated in better and most methods do not implement it correctly yet. Also, several PrimarySeqI methods (subseq(), trunc(), etc.) do not behave as expected and must be used with care.
Due to this, LocatableSeq functionality is to be refactored in a future BioPerl release. However, for alignment functionality it works adequately for the time being
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 listsSupport
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 the web:
https://redmine.open-bio.org/projects/bioperl/APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
start
Title : start
Usage : $obj->start($newval)
Function: Get/set the 1-based start position of this sequence in the original
sequence. '0' means before the original sequence starts.
Returns : value of start
Args : newvalue (optional)end
Title : end
Usage : $obj->end($newval)
Function: Get/set the 1-based end position of this sequence in the original
sequence. '0' means before the original sequence starts.
Returns : value of end
Args : newvalue (optional)
Note : although this is a get/set, it checks passed values against the
calculated end point ( derived from the sequence and based on
$GAP_SYMBOLS and possible frameshifts() ). If there is no match,
it will warn and set the proper value. Probably best used for
debugging proper sequence calculations.strand
Title : strand
Usage : $obj->strand($newval)
Function: return or set the strandedness
Returns : the value of the strandedness (-1, 0 or 1)
Args : the value of the strandedness (-1, 0 or 1)mapping
Title : mapping
Usage : $obj->mapping($newval)
Function: return or set the mapping indices (indicates # symbols/positions in
the source string mapping to # of coordinate positions)
Returns : two-element array (# symbols => # coordinate pos)
Args : two elements (# symbols => # coordinate pos); this can also be
passed in as an array reference of the two elements (as might be
passed upon FAST::Bio::LocatableSeq instantiation, for instance).frameshifts
Title : frameshifts
Usage : $obj->frameshifts($newval)
Function: get/set the frameshift hash, which contains sequence positions as
keys and the shift (-2, -1, 1, 2) as the value
Returns : hash
Args : hash or hash referenceget_nse
Title : get_nse
Usage :
Function: read-only name of form id/start-end
Example :
Returns :
Args :force_nse
Title : force_nse
Usage : $ls->force_nse()
Function: Boolean which forces get_nse() to build an NSE, regardless
of whether id(), start(), or end() is set
Returns : Boolean value
Args : (optional) Boolean (1 or 0)
Note : This will convert any passed value evaluating as TRUE/FALSE to 1/0
respectivelynum_gaps
Title : num_gaps
Usage :$self->num_gaps('.')
Function:Gets number of gaps in the sequence. The count excludes
leading or trailing gap characters.
Valid bioperl sequence characters are [A-Za-z\-\.\*]. Of
these, '.' and '-' are counted as gap characters unless an
optional argument specifies one of them.
Returns : number of internal gaps in the sequence.
Args : a gap character (optional)
Status : Stable
Note : replaces no_gapscolumn_from_residue_number
Title : column_from_residue_number
Usage : $col = $seq->column_from_residue_number($resnumber)
Function:
This function gives the position in the alignment
(i.e. column number) of the given residue number in the
sequence. For example, for the sequence
Seq1/91-97 AC..DEF.GH
column_from_residue_number(94) returns 6.
An exception is thrown if the residue number would lie
outside the length of the aligment
(e.g. column_from_residue_number( "Seq2", 22 )
Returns : A column number for the position of the
given residue in the given sequence (1 = first column)
Args : A residue number in the whole sequence (not just that
segment of it in the alignment)location_from_column
Title : location_from_column
Usage : $loc = $ali->location_from_column($column_number)
Function:
This function gives the residue number for a given position
in the alignment (i.e. column number) of the given. Gaps
complicate this process and force the output to be a
L<FAST::Bio::Location::Simple> where values can be undefined.
For example, for the sequence:
Seq/91-96 .AC..DEF.G.
location_from_column( 3 ) position 92
location_from_column( 4 ) position 92^93
location_from_column( 9 ) position 95^96
location_from_column( 1 ) position undef
An exact position returns a FAST::Bio::Location::Simple object
where where location_type() returns 'EXACT', if a position
is between bases location_type() returns 'IN-BETWEEN'.
Column before the first residue returns undef. Note that if
the position is after the last residue in the alignment,
that there is no guarantee that the original sequence has
residues after that position.
An exception is thrown if the column number is not within
the sequence.
Returns : FAST::Bio::Location::Simple or undef
Args : A column number
Throws : If column is not within the sequenceSee FAST::Bio::Location::Simple for more.
revcom
Title : revcom
Usage : $rev = $seq->revcom()
Function: Produces a new FAST::Bio::LocatableSeq object which
has the reversed complement of the sequence. For protein
sequences this throws an exception of "Sequence is a
protein. Cannot revcom"
Returns : A new FAST::Bio::LocatableSeq object
Args : nonetrunc
Title : trunc
Usage : $subseq = $myseq->trunc(10,100);
Function: Provides a truncation of a sequence,
Example :
Returns : a fresh FAST::Bio::PrimarySeqI implementing object
Args : Two integers denoting first and last columns of the
sequence to be included into sub-sequence.validate_seq
Title : validate_seq
Usage : if(! $seq->validate_seq($seq_str) ) {
print "sequence $seq_str is not valid for an object of
alphabet ",$seq->alphabet, "\n";
}
Function: Validates a given sequence string. A validating sequence string
must be accepted by seq(). A string that does not validate will
lead to an exception if passed to seq().
The implementation provided here does not take alphabet() into
account. Allowed are all letters (A-Z), numbers [0-9]
and common symbols used for gaps, stop codons, unknown residues,
and frameshifts, including '-','.','*','?','=',and '~'.
Example :
Returns : 1 if the supplied sequence string is valid for the object, and
0 otherwise.
Args : The sequence string to be validated.no_gap
Title : no_gaps
Usage : $self->no_gaps('.')
Function : Gets number of gaps in the sequence. The count excludes
leading or trailing gap characters.
Valid bioperl sequence characters are [A-Za-z\-\.\*]. Of
these, '.' and '-' are counted as gap characters unless an
optional argument specifies one of them.
Returns : number of internal gaps in the sequence.
Args : a gap character (optional)
Status : Deprecated (in favor of num_gaps()) no_sequences
Title : no_sequences
Usage : $gaps = $seq->no_sequences
Function : number of sequence in the sequence alignment
Returns : integer
Argument :
Status : Deprecated (in favor of num_sequences())