NAME
SimpleAlign - Multiple alignments held as a set of sequences
SYNOPSIS
$aln = new Bio::SimpleAlign;
$aln->read_MSF(\*STDIN);
$aln->write_fasta(\*STDOUT);INSTALLATION
This module is included with the central Bioperl distribution:
http://bio.perl.org/Core/Latest
ftp://bio.perl.org/pub/DISTFollow the installation instructions included in the README file.
DESCRIPTION
SimpleAlign handles multiple alignments of sequences. It is very permissive of types (it wont 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 manipulate an alignment (eg, truncate an alignment or remove columns that are all gaps). These functions are much better done by UnivAln by Georg Fuellen.
However for lightweight display/formatting - this is the one to use.
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.
vsns-bcd-perl@lists.uni-bielefeld.de - General discussion
vsns-bcd-perl-guts@lists.uni-bielefeld.de - Technically-oriented discussion
http://bio.perl.org/MailList.html - 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
Bio::Seq.pm - The biosequence object
http://bio.perl.org/Projects/modules.html - Online module documentation
http://bio.perl.org/Projects/SeqAlign/ - Bioperl sequence alignment project
http://bio.perl.org/ - Bioperl Project HomepageAPPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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)addSeq
Title : addSeq
Usage : $myalign->addSeq($newseq);
:
:
Function : Adds another sequence to the alignment
: *doesn't* align it - just adds it to the
: hashes
:
Returns : nothing
Argument : removeSeq
Title : removeSeq
Usage : $aln->removeSeq($seq);
Function : removes a single sequence from an alignmenteachSeq
Title : eachSeq
Usage : foreach $seq ( $align->eachSeq() )
:
:
Function : gets an array of Seq objects from the
: alignment
:
:
Returns : an array
Argument : nothingconsensus_string
Title : consensus_string
Usage : $str = $ali->consensus_string()
:
:
Function : Makes a consensus
:
:
:
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 : filehandlewrite_MSF
Title : write_MSF
Usage : $ali->write_MSF(\*FH)
:
:
Function : writes MSF format output
:
:
:
Returns :
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 : 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 : read_fasta
Title : read_fasta
Usage : $ali->read_fasta(\*INPUT)
:
:
Function : reads in a fasta formatted
: file for an alignment
:
:
Returns :
Argument : read_selex
Title : read_selex
Usage : $ali->read_selex(\*INPUT)
:
:
Function : reads selex (hmmer) format
: alignments
:
:
Returns :
Argument : read_mase
Title : read_mase
Usage : $ali->read_mase(\*INPUT)
:
:
Function : reads mase (seaview)
: formatted alignments
:
:
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_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 : write_Pfam
Title : write_Pfam
Usage : $ali->write_Pfam(\*OUTPUT)
:
:
Function : writes a Pfam/Mul formatted
: file
:
:
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 object 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 : 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 : 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 : 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 : 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 : uppercase
Title : uppercase()
Usage : $ali->uppercase()
:
:
Function : Sets all the sequences
: to uppercase
:
:
Returns :
Argument : no_sequences
Title : no_sequences
Usage : $depth = $ali->no_sequences
:
:
Function : number of sequence in the
: sequence alignment
:
:
Returns :
Argument : no_residues
Title : no_residues
Usage : $no = $ali->no_residues
:
:
Function : number of residues in total
: in the alignment
:
:
Returns :
Argument : purge
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)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 : Noneread_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 object