Bio::SimpleAlign - Multiple alignments held as a set of sequences # 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->score, "\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}; } 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 manipulations. However for lightweight display/formatting and minimal manipulation (e.g. removing 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 abbreviated 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. SimpleAlign is being slowly converted to bioperl coding standards, mainly by Ewan.

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 lists

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: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Ewan Birney, birney@sanger.ac.uk Allen Day, allenday@ucla.edu, Richard Adams, Richard.Adams@ed.ac.uk, David J. Evans, David.Evans@vir.gla.ac.uk, Heikki Lehvaslaiho, heikki@ebi.ac.uk, Allen Smith, allens@cpan.org, Jason Stajich, jason@bioperl.org, Anthony Underwood, aunderwood@phls.org.uk, Xintao Wei & Giri Narasimhan, giri@cs.fiu.edu Bio::LocatableSeq.pm The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : my $aln = new Bio::SimpleAlign(); Function : Creates a new simple align object Returns : Bio::SimpleAlign Args : -source => string representing the source program where this alignment came from These methods modify the MSE by adding, removing or shuffling complete sequences.

add_seq
Title : add_seq Usage : $myalign->add_seq($newseq); Function : Adds another sequence to the alignment. *Does not* align it - just adds it to the hashes. Returns : nothing Args : a Bio::LocatableSeq object order (optional) See Bio::LocatableSeq for more information

remove_seq
Title : remove_seq Usage : $aln->remove_seq($seq); Function : Removes a single sequence from an alignment Returns : Argument : a Bio::LocatableSeq object

purge
Title : purge Usage : $aln->purge(0.7); Function: Removes sequences above given sequence similarity This function will grind on large alignments. Beware! Example : Returns : An array of the removed sequences Args : float, threshold for similarity

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 : Methods returning one or more sequences objects.

each_seq
Title : each_seq Usage : foreach $seq ( $align->each_seq() ) Function : Gets an array of Seq objects from the alignment Returns : an array Argument :

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 :

each_seq_with_id
Title : each_seq_with_id Usage : foreach $seq ( $align->each_seq_with_id() ) 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 : a seq name

get_seq_by_pos
Title : get_seq_by_pos Usage : $seq = $aln->get_seq_by_pos(3) # third sequence from the alignment Function : Gets a sequence based on its position in the alignment. Numbering starts from 1. Sequence positions larger than no_sequences() will thow an error. Returns : a Bio::LocatableSeq object Args : positive integer for the sequence osition

seq_with_features
Title : seq_with_features Usage : $seq = $aln->seq_with_features(-pos => 1, -consensus => 60 -mask => sub { my $consensus = shift; for my $i (1..5){ my $n = 'N' x $i; my $q = '\?' x $i; while($consensus =~ /[^?]$q[^?]/){ $consensus =~ s/([^?])$q([^?])/$1$n$2/; } } return $consensus; } ); Function: produces a Bio::Seq object by first splicing gaps from -pos (by means of a splice_by_seq_pos() call), then creating features using non-? chars (by means of a consensus_string() call with stringency -consensus). Returns : a Bio::Seq object Args : -pos : required. sequence from which to build the Bio::Seq object -consensus : optional, defaults to consensus_string()'s default cutoff value -mask : optional, a coderef to apply to consensus_string()'s output before building features. this may be useful for closing gaps of 1bp by glossing over them with N, for instance The result of these methods are horizontal or vertical subsets of the current MSE.

select
Title : select Usage : $aln2 = $aln->select(1, 3) # three first sequences Function : Creates a new alignment from a continuous subset of sequences. Numbering starts from 1. Sequence positions larger than no_sequences() will thow an error. Returns : a Bio::SimpleAlign object Args : positive integer for the first sequence positive integer for the last sequence to include (optional)

select_noncont
Title : select_noncont Usage : $aln2 = $aln->select_noncont(1, 3) # first and 3rd sequences Function : Creates a new alignment from a subset of sequences. Numbering starts from 1. Sequence positions larger than no_sequences() will thow an error. Returns : a Bio::SimpleAlign object Args : array of integers for the sequences

slice
Title : slice Usage : $aln2 = $aln->slice(20, 30) Function : Creates a slice from the alignment inclusive of start and end columns. Sequences with no residues in the slice are excluded from the new alignment and a warning is printed. Slice beyond the length of the sequence does not do padding. Returns : a Bio::SimpleAlign object Args : positive integer for start column positive integer for end column

remove_columns
Title : remove_column Usage : $aln2 = $aln->remove_columns(['mismatch','weak']) Function : Creates an aligment with columns removed corresponding to the specified criteria. Returns : a L<Bio::SimpleAlign> object Args : array ref of types, 'match'|'weak'|'strong'|'mismatch'|'gaps'

remove_gaps
Title : remove_gaps Usage : $aln2 = $aln->remove_gaps('-') Function : Creates an aligment with gaps removed Returns : a L<Bio::SimpleAlign> object Args : a gap character(optional) if no specified, taken from $self->gap_char These methods affect characters in all sequences without changeing the alignment.

splice_by_seq_pos
Title : splice_by_seq_pos Usage : $status = splice_by_seq_pos(1); Function: splices all aligned sequences where the specified sequence has gaps. Example : Returns : 1 on success Args : position of sequence to splice by

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 : 'from' rexexp 'to' string

uppercase
Title : uppercase() Usage : $ali->uppercase() Function : Sets all the sequences to uppercase Returns : Argument :

cigar_line
Title : cigar_line() Usage : $align->cigar_line() Function : Generates a "cigar" line for each sequence in the alignment The format is simply A-1,60;B-1,1:4,60;C-5,10:12,58 where A,B,C,etc. are the sequence identifiers, and the numbers refer to conserved positions within the alignment Args : none

match_line
Title : match_line() Usage : $align->match_line() Function : Generates a match line - much like consensus string except that a line indicating the '*' for a match. Args : (optional) Match line characters ('*' by default) (optional) Strong match char (':' by default) (optional) Weak match char ('.' by default)

gap_line
Title : gap_line() Usage : $align->gap_line() Function : Generates a gap line - much like consensus string except that a line where '-' represents gap Args : (optional) gap line characters ('-' by default)

match
Title : match() Usage : $ali->match() Function : Goes through all columns and changes residues that are identical to residue in first sequence to match '.' character. Sets match_char. USE WITH CARE: Most MSE formats do not support match characters in sequences, so this is mostly for output only. NEXUS format (Bio::AlignIO::nexus) can handle it. Returns : 1 Argument : a match character, optional, defaults to '.'

unmatch
Title : unmatch() Usage : $ali->unmatch() Function : Undoes the effect of method match. Unsets match_char. Returns : 1 Argument : a match character, optional, defaults to '.' See match and match_char Methods for setting and reading the MSE attributes. Note that the methods defining character semantics depend on the user to set them sensibly. They are needed only by certain input/output methods. Unset them by setting to an empty string ('').

id
Title : id Usage : $myalign->id("Ig") Function : Gets/sets the id field of the alignment Returns : An id string Argument : An id string (optional)

missing_char
Title : missing_char Usage : $myalign->missing_char("?") Function : Gets/sets the missing_char attribute of the alignment It is generally recommended to set it to 'n' or 'N' for nucleotides and to 'X' for protein. Returns : An missing_char string, Argument : An missing_char string (optional)

match_char
Title : match_char Usage : $myalign->match_char('.') Function : Gets/sets the match_char attribute of the alignment Returns : An match_char string, Argument : An match_char string (optional)

gap_char
Title : gap_char Usage : $myalign->gap_char('-') Function : Gets/sets the gap_char attribute of the alignment Returns : An gap_char string, defaults to '-' Argument : An gap_char string (optional)

symbol_chars
Title : symbol_chars Usage : my @symbolchars = $aln->symbol_chars; Function: Returns all the seen symbols (other than gaps) Returns : array of characters that are the seen symbols Args : boolean to include the gap/missing/match characters These read only methods describe the MSE in various ways.

score
Title : score Usage : $str = $ali->score() Function : get/set a score of the alignment Returns : a score for the alignment Argument : an optional score to set

consensus_string
Title : consensus_string Usage : $str = $ali->consensus_string($threshold_percent) Function : Makes a strict consensus Returns : 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%)

consensus_iupac
Title : consensus_iupac Usage : $str = $ali->consensus_iupac() Function : Makes a consensus using IUPAC ambiguity codes from DNA and RNA. The output is in upper case except when gaps in a column force output to be in lower case. Note that if your alignment sequences contain a lot of IUPAC ambiquity codes you often have to manually set alphabet. Bio::PrimarySeq::_guess_type thinks they indicate a protein sequence. Returns : consensus string Argument : none Throws : on protein sequences

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
Title : length() Usage : $len = $ali->length() Function : Returns the maximum length of the alignment. To be sure the alignment is a block, use is_flush Returns : Argument :

maxdisplayname_length
Title : maxdisplayname_length Usage : $ali->maxdisplayname_length() Function : Gets the maximum length of the displayname in the alignment. Used in writing out various MSE formats. Returns : integer Argument :

no_residues
Title : no_residues Usage : $no = $ali->no_residues Function : number of residues in total in the alignment Returns : integer Argument :

no_sequences
Title : no_sequences Usage : $depth = $ali->no_sequences Function : number of sequence in the sequence alignment Returns : integer Argument :

average_percentage_identity
Title : average_percentage_identity Usage : $id = $align->average_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 : None Notes : This method implemented by Kevin Howe calculates a figure that is designed to be similar to the average pairwise identity of the alignment (identical in the absence of gaps), without having to explicitly calculate pairwise identities proposed by Richard Durbin. Validated by Ewan Birney ad Alex Bateman.

percentage_identity
Title : percentage_identity Usage : $id = $align->percentage_identity Function: The function calculates the average percentage identity (aliased for average_percentage_identity) Returns : The average percentage identity Args : None

overall_percentage_identity
Title : percentage_identity Usage : $id = $align->percentage_identity Function: The function calculates the percentage identity of the conserved columns Returns : The percentage identity of the conserved columns Args : None Methods to map a sequence position into an alignment column and back. column_from_residue_number() does the former. The latter is really a property of the sequence object and can done using Bio::LocatableSeq::location_from_column: # select somehow a sequence from the alignment, e.g. my $seq = $aln->get_seq_by_pos(1); #$loc is undef or Bio::LocationI object my $loc = $seq->location_from_column(5);

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 ) Note: If the the parent sequence is represented by more than one alignment sequence and the residue number is present in them, this method finds only the first one. Returns : A column number for the position in the alignment of the given residue in the given sequence (1 = first column) Args : A sequence id/name (not a name/start-end) A residue number in the whole sequence (not just that segment of it in the alignment) Methods to manipulate the display name. The default name based on the sequence id and subsequence positions can be overridden in various ways.

displayname
Title : displayname Usage : $myalign->displayname("Ig", "IgA") Function : Gets/sets the display name of a sequence in the alignment : Returns : A display name string Argument : name of the sequence displayname of the sequence (optional)

set_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 : 1 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 :

source
Title : source Usage : $obj->source($newval) Function: sets the Alignment source program Example : Returns : value of source Args : newvalue (optional)