NAME
SimpleAlign - Multiple alignments held as a set of sequences
SYNOPSIS
# use Bio::AlignIO to read in the alignment
$str = Bio::AlignIO->new('-file' => 't/data/testaln.pfam');
$aln = $str->next_aln();
# some descriptors
print $aln->length, "\n";
print $aln->no_residues, "\n";
print $aln->is_flush, "\n";
print $aln->no_sequences, "\n";
print $aln->percentage_identity, "\n";
print $aln->consensus_string(50), "\n";
# find the position in the alignment for a sequence location
$pos = $aln->column_from_residue_number('1433_LYCES', 14); # = 6;
# extract sequences and check values for the alignment column $pos
foreach $seq ($aln->each_seq) {
$res = $seq->subseq($pos, $pos);
$count{$res}++;
}
foreach $res (keys %count) {
printf "Res: %s Count: %2d\n", $res, $count{$res};
}DESCRIPTION
SimpleAlign handles multiple alignments of sequences. It is very permissive of types (it won\'t insist on things being all same length etc): really it is a SequenceSet explicitly held in memory with a whole series of built in manipulations and especially file format systems for read/writing alignments.
SimpleAlign basically views an alignment as an immutable block of text. SimpleAlign *is not* the object to be using if you want to perform complex alignment alignment manipulations. These functions are much better done by UnivAln by Georg Fuellen.
However for lightweight display/formatting and minimal manipulation (e.g. removiung all-gaps columns) - this is the one to use.
SimpleAlign uses a subclass of Bio::PrimarySeq class Bio::LocatableSeq to store its sequences. These are subsequences with a start and end positions in the parent reference sequence.
Tricky concepts. SimpleAlign expects name,start,end to be 'unique' in the alignment, and this is the key for the internal hashes. (name,start,end is abreviated nse in the code). However, in many cases people don\'t want the name/start-end to be displayed: either multiple names in an alignment or names specific to the alignment (ROA1_HUMAN_1, ROA1_HUMAN_2 etc). These names are called 'displayname', and generally is what is used to print out the alignment. They default to name/start-end
The SimpleAlign Module came from Ewan Birney\'s Align module
PROGRESS
SimpleAlign is being slowly converted to bioperl coding standards, mainly by Ewan.
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/MailList.shtml - About the mailing listsReporting 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:
bioperl-bugs@bio.perl.org
http://bio.perl.org/bioperl-bugs/AUTHOR
Ewan Birney, birney@sanger.ac.uk
SEE ALSO
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
addSeq
Title : addSeq
Usage : $myalign->addSeq($newseq);
:
:
Function : Adds another sequence to the alignment
: *does not* align it - just adds it to the
: hashes
:
Returns : nothing
Argument :column_from_residue_number
Title : column_from_residue_number
Usage : $col = $ali->column_from_residue_number( $seqname, $resnumber)
Function:
This function gives the position in the alignment (i.e. column number) of
the given residue number in the sequence with the given name. For example,
for the alignment
Seq1/91-97 AC..DEF.GH
Seq2/24-30 ACGG.RTY..
Seq3/43-51 AC.DDEFGHI
column_from_residue_number( "Seq1", 94 ) returns 5.
column_from_residue_number( "Seq2", 25 ) returns 2.
column_from_residue_number( "Seq3", 50 ) returns 9.
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 postion in the alignment of the
given residue in the given sequence (1 = first column)
Args :
A sequence name (not a name/start-end)
A residue number in the whole sequence (not just that segment of it
in the alignment)consensus_string
Title : consensus_string
Usage : $str = $ali->consensus_string($threshold_percent)
Function : Makes a consensus
Returns :
Argument : Optional treshold ranging from 0 to 100. If consensus residue appears in
fewer than threshold % of the sequences at a given location
consensus_string will return a "?" at that location rather than the consensus
letter. (Default value = 0%)consensus_aa
Title : consensus_aa
Usage : $consensus_residue = $ali->consensus_aa($residue_number, $threshold_percent)
Function : Makes a consensus
Returns :
Argument :
Argument : Optional treshold ranging from 0 to 100.
The consensus residue has to appear at least threshold %
of the sequences at a given location, otherwise a '?'
character will be placed at that location.
(Default value = 0%)each_alphabetically
Title : each_alphabetically
Usage : foreach $seq ( $ali->each_alphabetically() )
:
:
Function : returns an array of sequence object sorted
: alphabetically by name and then by start point
:
: Does not change the order of the alignment
Returns :
Argument :eachSeq
Title : eachSeq
Usage : foreach $seq ( $align->eachSeq() )
:
:
Function : gets an array of Seq objects from the
: alignment
:
:
Returns : an array
Argument : nothingeachSeqWithId
Title : eachSeqWithId
Usage : foreach $seq ( $align->eachSeqWithName() )
:
:
Function : gets an array of Seq objects from the
: alignment, the contents being those sequences
: with the given name (there may be more than one
:
Returns : an array
Argument : nothingid
Title : id
Usage : $myalign->id("Ig")
Function : Gets/sets the id field of the alignment
:
Returns : An id string
Argument : An id string (optional)is_flush
Title : is_flush
Usage : if( $ali->is_flush() )
:
:
Function : Tells you whether the alignment
: is flush, ie all of the same length
:
:
Returns : 1 or 0
Argument :length_aln
Title : length_aln()
Usage : $len = $ali->length_aln()
:
:
Function : returns the maximum length of the alignment.
: To be sure the alignment is a block, use is_flush
:
:
Returns :
Argument :map_chars
Title : map_chars
Usage : $ali->map_chars('\.','-')
:
:
Function : does a s/$arg1/$arg2/ on
: the sequences. Useful for
: gap characters
:
: Notice that the from (arg1) is interpretted
: as a regex, so be careful about quoting meta
: characters (eg $ali->map_chars('.','-') wont
: do what you want)
Returns :
Argument :no_residues
Title : no_residues
Usage : $no = $ali->no_residues
:
:
Function : number of residues in total
: in the alignment
:
:
Returns :
Argument :no_sequences
Title : no_sequences
Usage : $depth = $ali->no_sequences
:
:
Function : number of sequence in the
: sequence alignment
:
:
Returns :
Argument :percentage_identity
Title : percentage_identity
Usage : $id = $align->percentage_identity
Function:
The function uses a fast method to calculate the average percentage identity of the alignment
Returns : The average percentage identity of the alignment
Args : Nonepurge
Title : purge
Usage : $aln->purge(0.7);
Function: removes sequences above whatever %id
Example :
Returns : An array of the removed sequences
Arguments
This function will grind on large alignments. Beware!
(perhaps not ideally implemented)read_fasta
Title : read_fasta
Usage : $ali->read_fasta(\*INPUT)
:
:
Function : reads in a fasta formatted
: file for an alignment
:
:
Returns :
Argument :read_mase
Title : read_mase
Usage : $ali->read_mase(\*INPUT)
:
:
Function : reads mase (seaview)
: formatted alignments
:
:
Returns :
Argument :read_MSF
Title : read_MSF
Usage : $al->read_MSF(\*STDIN);
Function: reads MSF formatted files. Tries to read *all* MSF
It reads all non whitespace characters in the alignment
area. For MSFs with weird gaps (eg ~~~) map them by using
$al->map_chars('~','-');
Example :
Returns :
Args : filehandleread_Pfam
Title : read_Pfam
Usage : $ali->read_Pfam(\*INPUT)
:
:
Function : reads a Pfam formatted
: Alignment (Mul format).
: - this is the format used by Belvu
:
Returns :
Argument :read_Pfam_file
Title : read_Pfam_file
Usage : $ali->read_Pfam_file("thisfile");
:
Function : opens a filename, reads
: a Pfam (mul) formatted alignment
:
:
:
Returns :
Argument :read_Prodom
Title : read_Prodom
Usage : $ali->read_Prodom( $file )
Function: Reads in a Prodom format alignment
Returns :
Args : A filehandle glob or ref. to a filehandle objectread_selex
Title : read_selex
Usage : $ali->read_selex(\*INPUT)
:
:
Function : reads selex (hmmer) format
: alignments
:
:
Returns :
Argument :read_stockholm
Title : read_stockholm
Usage : $ali->read_stockholm(\*INPUT)
:
:
Function : reads stockholm format alignments
:
:
Returns :
Argument :removeSeq
Title : removeSeq
Usage : $aln->removeSeq($seq);
Function : removes a single sequence from an alignmentset_displayname_count
Title : set_displayname_count
Usage : $ali->set_displayname_count
:
:
Function : sets the names to be name_#
: where # is the number of times this
: name has been used.
:
Returns :
Argument :set_displayname_flat
Title : set_displayname_flat
Usage : $ali->set_displayname_flat()
:
:
Function : Makes all the sequences be displayed
: as just their name, not name/start-end
:
:
Returns :
Argument :set_displayname_normal
Title : set_displayname_normal
Usage : $ali->set_displayname_normal()
:
:
Function : Makes all the sequences be displayed
: as name/start-end
:
:
Returns :
Argument :sort_alphabetically
Title : sort_alphabetically
Usage : $ali->sort_alphabetically
:
:
Function : changes the order of the alignemnt
: to alphabetical on name followed by
: numerical by number
:
Returns :
Argument :uppercase
Title : uppercase()
Usage : $ali->uppercase()
:
:
Function : Sets all the sequences
: to uppercase
:
:
Returns :
Argument :write_clustalw
Title : write_clustalw
Usage : $ali->write_clustalw
:
:
Function : writes a clustalw formatted
: (.aln) file
:
:
Returns :
Argument :write_fasta
Title : write_fasta
Usage : $ali->write_fasta(\*OUTPUT)
:
:
Function : writes a fasta formatted alignment
:
Returns :
Argument : reference-to-glob to file or filehandle objectwrite_MSF
Title : write_MSF
Usage : $ali->write_MSF(\*FH)
:
:
Function : writes MSF format output
:
:
:
Returns :
Argument :write_Pfam
Title : write_Pfam
Usage : $ali->write_Pfam(\*OUTPUT)
:
:
Function : writes a Pfam/Mul formatted
: file
:
:
Returns :
Argument :write_selex
Title : write_selex
Usage : $ali->write_selex(\*OUTPUT)
:
:
Function : writes a selex (hmmer) formatted alignment
:
Returns :
Argument : reference-to-glob to file or filehandle object