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(); # Describe print $aln->length; print $aln->no_residues; print $aln->is_flush; print $aln->no_sequences; print $aln->score; print $aln->percentage_identity; print $aln->consensus_string(50); # 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}; } # Manipulate $aln->remove_seq($seq); $mini_aln = $aln->slice(20,30); # get a block of columns $mini_aln = $aln->select_noncont(1,3,5,7,11); # get single columns $new_aln = $aln->remove_columns([20,30]); # remove by position $new_aln = $aln->remove_columns(['mismatch']); # remove by property # Analyze $str = $aln->consensus_string($threshold_percent); $str = $aln->match_line(); $str = $aln->cigar_line() $id = $aln->percentage_identity;
See the module documentation for details and more methods.
SimpleAlign is an object that handles a multiple sequence alignment (MSA). It is very permissive of types (it does not insist on sequences being all same length, for example). Think of it as a set of sequences with a whole series of built-in manipulations and methods for reading and writing alignments.
SimpleAlign uses Bio::LocatableSeq, a subclass of Bio::PrimarySeq, to store its sequences. These are subsequences with a start and end positions in the parent reference sequence. Each sequence in the SimpleAlign object is a Bio::LocatableSeq.
SimpleAlign expects the combination of name, start, and end for a given sequence to be unique in the alignment, and this is the key for the internal hashes (name, start, end are abbreviated nse in the code). However, in some cases people do not 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.
nse
displayname
The SimpleAlign Module is derived from the Align module by Ewan Birney.
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
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:
http://bugzilla.open-bio.org/
Ewan Birney, birney@ebi.ac.uk
Allen Day, allenday-at-ucla.edu, Richard Adams, Richard.Adams-at-ed.ac.uk, David J. Evans, David.Evans-at-vir.gla.ac.uk, Heikki Lehvaslaiho, heikki-at-bioperl-dot-org, Allen Smith, allens-at-cpan.org, Jason Stajich, jason-at-bioperl.org, Anthony Underwood, aunderwood-at-phls.org.uk, Xintao Wei & Giri Narasimhan, giri-at-cs.fiu.edu Brian Osborne, bosborne at alum.mit.edu
Bio::LocatableSeq
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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 MSA by adding, removing or shuffling complete sequences.
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
Title : remove_seq Usage : $aln->remove_seq($seq); Function : Removes a single sequence from an alignment Returns : Argument : a Bio::LocatableSeq object
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
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 :
Title : set_new_reference Usage : $aln->set_new_reference(3 or 'B31'): Select the 3rd sequence, or the sequence whoes name is "B31" (full, exact, and case-sensitive), as the reference (1st) sequence Function : Change/Set a new reference (i.e., the first) sequence Returns : a new Bio::SimpleAlign object. Throws an exception if designated sequence not found Argument : a positive integer of sequence order, or a sequence name in the original alignment
Title : uniq_seq Usage : $aln->uniq_seq(): Remove identical sequences in in the alignment. Ambiguous base ("N", "n") and leading and ending gaps ("-") are NOT counted as differences. Function : Make a new alignment of unique sequence types (STs) Returns : 1. a new Bio::SimpleAlign object (all sequences renamed as "ST") 2. ST of each sequence in STDERR Argument : None
Methods returning one or more sequences objects.
Title : each_seq Usage : foreach $seq ( $align->each_seq() ) Function : Gets a Seq object from the alignment Returns : Seq object Argument :
Title : each_alphabetically Usage : foreach $seq ( $ali->each_alphabetically() ) Function : Returns a sequence object, but the objects are returned in alphabetically sorted order. Does not change the order of the alignment. Returns : Seq object Argument :
Title : each_seq_with_id Usage : foreach $seq ( $align->each_seq_with_id() ) Function : Gets a Seq objects from the alignment, the contents being those sequences with the given name (there may be more than one) Returns : Seq object Argument : a seq name
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
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 1 bp by masking over them with N, for instance
The result of these methods are horizontal or vertical subsets of the current MSA.
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)
Title : select_noncont Usage : $aln2 = $aln->select_noncont(1, 3) # 1st 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
Title : slice Usage : $aln2 = $aln->slice(20,30) Function : Creates a slice from the alignment inclusive of start and end columns, and the first column in the alignment is denoted 1. 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, optional boolean which if true will keep gap-only columns in the newly created slice. Example: $aln2 = $aln->slice(20,30,1)
Title : remove_columns Usage : $aln2 = $aln->remove_columns(['mismatch','weak']) or $aln2 = $aln->remove_columns([0,0],[6,8]) Function : Creates an aligment with columns removed corresponding to the specified type or by specifying the columns by number. Returns : Bio::SimpleAlign object Args : Array ref of types ('match'|'weak'|'strong'|'mismatch'|'gaps'| 'all_gaps_columns') or array ref where the referenced array contains a pair of integers that specify a range. The first column is 0,
Title : remove_gaps Usage : $aln2 = $aln->remove_gaps Function : Creates an aligment with gaps removed Returns : a Bio::SimpleAlign object Args : a gap character(optional) if none specified taken from $self->gap_char, [optional] $all_gaps_columns flag (1 or 0, default is 0) indicates that only all-gaps columns should be deleted
Used from method remove_columns in most cases. Set gap character using gap_char().
These methods affect characters in all sequences without changing the alignment.
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
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
Title : uppercase() Usage : $ali->uppercase() Function : Sets all the sequences to uppercase Returns : Argument :
Title : cigar_line() Usage : %cigars = $align->cigar_line() Function : Generates a "cigar" (Compact Idiosyncratic Gapped Alignment Report) line for each sequence in the alignment. Examples are "1,60" or "5,10:12,58", where the numbers refer to conserved positions within the alignment. The keys of the hash are the NSEs (name/start/end) assigned to each sequence. Args : none Returns : Hash of strings (cigar lines)
Title : match_line() Usage : $line = $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) Returns : String
Title : gap_line() Usage : $line = $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) Returns : string
Title : all_gap_line() Usage : $line = $align->all_gap_line() Function : Generates a gap line - much like consensus string except that a line where '-' represents all-gap column Args : (optional) gap line characters ('-' by default) Returns : string
Title : gap_col_matrix() Usage : my $cols = $align->gap_col_matrix() Function : Generates an array of hashes where each entry in the array is a hash reference with keys of all the sequence names and and value of 1 or 0 if the sequence has a gap at that column Args : (optional) gap line characters ($aln->gap_char or '-' by default)
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 MSA 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 '.'
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 MSA 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 ('').
Title : id Usage : $myalign->id("Ig") Function : Gets/sets the id field of the alignment Returns : An id string Argument : An id string (optional)
Title : accession Usage : $myalign->accession("PF00244") Function : Gets/sets the accession field of the alignment Returns : An acc string Argument : An acc string (optional)
Title : description Usage : $myalign->description("14-3-3 proteins") Function : Gets/sets the description field of the alignment Returns : An description string Argument : An description string (optional)
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)
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)
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)
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 MSA in various ways.
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
Title : consensus_string Usage : $str = $ali->consensus_string($threshold_percent) Function : Makes a strict consensus Returns : Consensus string 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%)
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
Title : consensus_meta Usage : $seqmeta = $ali->consensus_meta() Function : Returns a Bio::Seq::Meta object containing the consensus strings derived from meta data analysis. Returns : Bio::Seq::Meta Argument : Bio::Seq::Meta Throws : non-MetaI object
Title : is_flush Usage : if ( $ali->is_flush() ) Function : Tells you whether the alignment : is flush, i.e. all of the same length Returns : 1 or 0 Argument :
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 : Integer Argument :
Title : maxdisplayname_length Usage : $ali->maxdisplayname_length() Function : Gets the maximum length of the displayname in the alignment. Used in writing out various MSA formats. Returns : integer Argument :
Title : max_metaname_length Usage : $ali->max_metaname_length() Function : Gets the maximum length of the meta name tags in the alignment for the sequences and for the alignment. Used in writing out various MSA formats. Returns : integer Argument : None
Title : no_residues Usage : $no = $ali->no_residues Function : number of residues in total in the alignment Returns : integer Argument :
Title : no_sequences Usage : $depth = $ali->no_sequences Function : number of sequence in the sequence alignment Returns : integer Argument :
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.
Title : percentage_identity Usage : $id = $align->percentage_identity Function: The function calculates the average percentage identity (aliased to average_percentage_identity) Returns : The average percentage identity Args : None
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);
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.DDEF.GHI column_from_residue_number( "Seq1", 94 ) returns 6. column_from_residue_number( "Seq2", 25 ) returns 2. column_from_residue_number( "Seq3", 50 ) returns 10. 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.
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)
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 : 1, on success Argument :
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 :
Title : set_displayname_normal Usage : $ali->set_displayname_normal() Function : Makes all the sequences be displayed as name/start-end Returns : 1, on success Argument :
Title : source Usage : $obj->source($newval) Function: sets the Alignment source program Example : Returns : value of source Args : newvalue (optional)
Title : annotation Usage : $ann = $aln->annotation or $aln->annotation($ann) Function: Gets or sets the annotation Returns : Bio::AnnotationCollectionI object Args : None or Bio::AnnotationCollectionI object
See Bio::AnnotationCollectionI and Bio::Annotation::Collection for more information
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.