#
# BioPerl module for Bio::AlignIO::phylip
#
# Copyright Heikki Lehvaslaiho
#
=head1 NAME
Bio::AlignIO::phylip - PHYLIP format sequence input/output stream
=head1 SYNOPSIS
# Do not use this module directly. Use it via the Bio::AlignIO class.
use Bio::AlignIO;
use Bio::SimpleAlign;
#you can set the name length to something other than the default 10
#if you use a version of phylip (hacked) that accepts ids > 10
my $phylipstream = Bio::AlignIO->new(-format => 'phylip',
-fh => \*STDOUT,
-idlength=>30);
# convert data from one format to another
my $gcgstream = Bio::AlignIO->new(-format => 'msf',
-file => 't/data/cysprot1a.msf');
while( my $aln = $gcgstream->next_aln ) {
$phylipstream->write_aln($aln);
}
# do it again with phylip sequential format format
$phylipstream->interleaved(0);
# can also initialize the object like this
$phylipstream = Bio::AlignIO->new(-interleaved => 0,
-format => 'phylip',
-fh => \*STDOUT,
-idlength=>10);
$gcgstream = Bio::AlignIO->new(-format => 'msf',
-file => 't/data/cysprot1a.msf');
while( my $aln = $gcgstream->next_aln ) {
$phylipstream->write_aln($aln);
}
=head1 DESCRIPTION
This object can transform Bio::SimpleAlign objects to and from PHYLIP
format. By default it works with the interleaved format. By specifying
the flag -interleaved =E<gt> 0 in the initialization the module can
read or write data in sequential format.
Long IDs up to 50 characters are supported by flag -longid =E<gt>
1. ID strings can be surrounded by single quoted. They are mandatory
only if the IDs contain spaces.
=head1 FEEDBACK
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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/
=head1 AUTHORS - Heikki Lehvaslaiho and Jason Stajich
Email: heikki at ebi.ac.uk
Email: jason at bioperl.org
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::AlignIO::phylip;
use vars qw($DEFAULTIDLENGTH $DEFAULTLINELEN $DEFAULTTAGLEN);
use strict;
use Bio::SimpleAlign;
use POSIX; # for the rounding call
use base qw(Bio::AlignIO);
BEGIN {
$DEFAULTIDLENGTH = 10;
$DEFAULTLINELEN = 60;
$DEFAULTTAGLEN = 10;
}
=head2 new
Title : new
Usage : my $alignio = Bio::AlignIO->new(-format => 'phylip'
-file => '>file',
-idlength => 10,
-idlinebreak => 1);
Function: Initialize a new L<Bio::AlignIO::phylip> reader or writer
Returns : L<Bio::AlignIO> object
Args : [specific for writing of phylip format files]
-idlength => integer - length of the id (will pad w/
spaces if needed)
-interleaved => boolean - whether interleaved
or sequential format required
-line_length => integer of how long a sequence lines should be
-idlinebreak => insert a line break after the sequence id
so that sequence starts on the next line
-flag_SI => whether or not write a "S" or "I" just after
the num.seq. and line len., in the first line
-tag_length => integer of how long the tags have to be in
each line between the space separator. set it
to 0 to have 1 tag only.
-wrap_sequential => boolean for whether or not sequential
format should be broken up or a single line
default is false (single line)
-longid => boolean for allowing arbitrary long IDs (default is false)
=cut
sub _initialize {
my($self,@args) = @_;
$self->SUPER::_initialize(@args);
my ($interleave,$linelen,$idlinebreak,
$idlength, $flag_SI, $tag_length,$ws, $longid) =
$self->_rearrange([qw(INTERLEAVED
LINE_LENGTH
IDLINEBREAK
IDLENGTH
FLAG_SI
TAG_LENGTH
WRAP_SEQUENTIAL
LONGID)],@args);
$self->interleaved($interleave ? 1 : 0) if defined $interleave;
$self->idlength($idlength || $DEFAULTIDLENGTH);
$self->id_linebreak(1) if( $idlinebreak );
$self->line_length($linelen) if defined $linelen && $linelen > 0;
$self->flag_SI(1) if ( $flag_SI );
$self->tag_length($tag_length) if ( $tag_length || $DEFAULTTAGLEN );
$self->wrap_sequential($ws ? 1 : 0);
$self->longid($longid ? 1 : 0);
1;
}
=head2 next_aln
Title : next_aln
Usage : $aln = $stream->next_aln()
Function: returns the next alignment in the stream.
Throws an exception if trying to read in PHYLIP
sequential format.
Returns : L<Bio::SimpleAlign> object
Args :
=cut
sub next_aln {
my $self = shift;
my $entry;
my ($seqcount, $residuecount, %hash, $name,$str,
@names,$seqname,$start,$end,$count,$seq);
my $aln = Bio::SimpleAlign->new(-source => 'phylip');
# First, parse up through the header.
# If we see a non-blank line that isn't the seqcount and residuecount line
# then bail out of next_aln (return)
while ($entry = $self->_readline) {
if ($entry =~ /^\s?$/) {
next;
} elsif ($entry =~ /\s*(\d+)\s+(\d+)/) {
($seqcount, $residuecount) = ($1, $2);
last;
} else {
$self->warn ("Failed to parse PHYLIP: Did not see a sequence count and residue count.");
return;
}
}
# First alignment section. We expect to see a name and (part of) a sequence.
my $idlen = $self->idlength;
$count = 0;
while ($entry = $self->_readline) {
if ($entry =~ /^\s?$/) { # eat the newlines
next;
}
# Names can be in a few different formats:
# 1. they can be traditional phylip: 10 chars long, period. If this is the case, that name can have spaces.
# 2. they can be hacked with a long ID, as passed in with the flag -longid.
# 3. if there is a long ID, the name can have spaces as long as it is wrapped in single quotes.
if ($self->longid()) { # 2 or 3
if ($entry =~ /^'(.+)'\s+(.+)$/) { # 3. name has single quotes.
$name = $1;
$str = $2;
} else { # 2. name does not have single quotes, so should not have spaces.
# therefore, the first part of the line is the name and the rest is the seq.
# make sure that the line does not lead with extra spaces.
$entry =~ s/^\s+//;
($name, $str) = split (/\s+/,$entry, 2);
}
} else { # 1. traditional phylip.
$entry =~ /^(.{10})\s+(.+)$/;
$name = $1;
$str = $2;
$name =~ s/\s+$//; # eat any trailing spaces
$name =~ s/\s+/_/g;
}
push @names, $name;
#clean sequence of spaces:
$str =~ s/\s+//g;
# are we sequential? If so, we should keep adding to the sequence until we've got all the residues.
if (($self->interleaved) == 0) {
while (length($str) < $residuecount) {
$entry = $self->_readline;
$str .= $entry;
$str =~ s/\s+//g;
if ($entry =~ /^\s*$/) { # we ran into a newline before we got a complete sequence: bail!
$self->warn("Failed to parse PHYLIP: Sequence $name was shorter than expected: " . length($str) . " instead of $residuecount.");
last;
}
}
}
$hash{$count} = $str;
$count++;
# if we've read as many seqs as we're supposed to, move on.
if ($count == $seqcount) {
last;
}
}
# if we are interleaved, we're going to keep seeing chunks of sequence until we get all of it.
if ($self->interleaved) {
while (length($hash{$seqcount-1}) < $residuecount) {
$count = 0;
while ($entry = $self->_readline) {
if ($entry =~ /^\s*$/) { # eat newlines
if ($count != 0) { # there was a newline at an unexpected place!
$self->warn("Failed to parse PHYLIP: Interleaved file is missing a segment: saw $count, expected $seqcount.");
return;
}
next;
} else { # start taking in chunks
$entry =~ s/\s//g;
$hash{$count} .= $entry;
$count++;
}
if ($count >= $seqcount) { # we've read all of the sequences for this chunk, so move on.
last;
}
}
}
}
if ((scalar @names) != $seqcount) {
$self->warn("Failed to parse PHYLIP: Did not see the correct number of seqs: saw " . scalar(@names) . ", expected $seqcount.");
return;
}
for ($count=0; $count<$seqcount; $count++) {
$str = $hash{$count};
my $seqname = $names[$count];
if (length($str) != $residuecount) {
$self->warn("Failed to parse PHYLIP: Sequence $seqname was the wrong length: " . length($str) . " instead of $residuecount.");
}
$seq = Bio::LocatableSeq->new('-seq' => $hash{$count},
'-display_id' => $seqname);
$aln->add_seq($seq);
}
return $aln;
}
=head2 write_aln
Title : write_aln
Usage : $stream->write_aln(@aln)
Function: writes the $aln object into the stream in phylip format
Returns : 1 for success and 0 for error
Args : L<Bio::Align::AlignI> object
=cut
sub write_aln {
my ($self,@aln) = @_;
my $count = 0;
my $wrapped = 0;
my $maxname;
my $width = $self->line_length();
my ($length,$date,$name,$seq,$miss,$pad,
%hash,@arr,$tempcount,$index,$idlength,$flag_SI,$line_length, $tag_length);
foreach my $aln (@aln) {
if( ! $aln || ! $aln->isa('Bio::Align::AlignI') ) {
$self->warn("Must provide a Bio::Align::AlignI object when calling write_aln");
next;
}
$self->throw("All sequences in the alignment must be the same length")
unless $aln->is_flush(1) ;
$flag_SI = $self->flag_SI();
$aln->set_displayname_flat(); # plain
$length = $aln->length();
if ($flag_SI) {
if ($self->interleaved() ) {
$self->_print (sprintf(" %s %s I\n", $aln->num_sequences, $aln->length));
} else {
$self->_print (sprintf(" %s %s S\n", $aln->num_sequences, $aln->length));
}
} else {
$self->_print (sprintf(" %s %s\n", $aln->num_sequences, $aln->length));
}
$idlength = $self->idlength();
$line_length = $self->line_length();
$tag_length = $self->tag_length();
foreach $seq ( $aln->each_seq() ) {
$name = $aln->displayname($seq->get_nse);
if ($self->longid) {
$self->warn("The length of the name is over 50 chars long [$name]")
if length($name) > 50;
$name = "'$name' "
} else {
$name = substr($name, 0, $idlength) if length($name) > $idlength;
$name = sprintf("%-".$idlength."s",$name);
if( $self->interleaved() ) {
$name .= ' ' ;
} elsif( $self->id_linebreak) {
$name .= "\n";
}
}
#phylip needs dashes not dots
my $seq = $seq->seq();
$seq =~ s/\./-/g;
$hash{$name} = $seq;
push(@arr,$name);
}
if( $self->interleaved() ) {
my $numtags;
if ($tag_length <= $line_length) {
$numtags = floor($line_length/$tag_length);
$line_length = $tag_length*$numtags;
} else {
$numtags = 1;
}
while( $count < $length ) {
# there is another block to go!
foreach $name ( @arr ) {
my $dispname = $name;
$dispname = '' if $wrapped;
$self->_print (sprintf("%".($idlength+3)."s",$dispname));
$tempcount = $count;
$index = 0;
$self->debug("residue count: $count\n") if ($count%100000 == 0);
while( ($tempcount + $tag_length < $length) &&
($index < $numtags) ) {
$self->_print (sprintf("%s ",substr($hash{$name},
$tempcount,
$tag_length)));
$tempcount += $tag_length;
$index++;
}
# last
if( $index < $numtags) {
# space to print!
$self->_print (sprintf("%s",substr($hash{$name},
$tempcount)));
$tempcount += $tag_length;
}
$self->_print ("\n");
}
$self->_print ("\n");
$count = $tempcount;
$wrapped = 1;
}
} else {
foreach $name ( @arr ) {
my $dispname = $name;
my $line = sprintf("%s%s\n",$dispname,$hash{$name});
if( $self->wrap_sequential ) {
$line =~ s/(.{1,$width})/$1\n/g;
}
$self->_print ($line);
}
}
}
$self->flush if $self->_flush_on_write && defined $self->_fh;
return 1;
}
=head2 interleaved
Title : interleaved
Usage : my $interleaved = $obj->interleaved
Function: Get/Set Interleaved status
Returns : boolean
Args : boolean
=cut
sub interleaved {
my ($self,$value) = @_;
if( defined $value ) {
if ($value) {$self->{'_interleaved'} = 1 }
else {$self->{'_interleaved'} = 0 }
}
return 1 unless defined $self->{'_interleaved'};
return $self->{'_interleaved'};
}
=head2 flag_SI
Title : flag_SI
Usage : my $flag = $obj->flag_SI
Function: Get/Set if the Sequential/Interleaved flag has to be shown
after the number of sequences and sequence length
Example :
Returns : boolean
Args : boolean
=cut
sub flag_SI{
my ($self,$value) = @_;
my $previous = $self->{'_flag_SI'};
if( defined $value ) {
$self->{'_flag_SI'} = $value;
}
return $previous;
}
=head2 idlength
Title : idlength
Usage : my $idlength = $obj->idlength
Function: Get/Set value of id length
Returns : string
Args : string
=cut
sub idlength {
my($self,$value) = @_;
if (defined $value){
$self->{'_idlength'} = $value;
}
return $self->{'_idlength'};
}
=head2 line_length
Title : line_length
Usage : $obj->line_length($newval)
Function:
Returns : value of line_length
Args : newvalue (optional)
=cut
sub line_length{
my ($self,$value) = @_;
if( defined $value) {
$self->{'_line_length'} = $value;
}
return $self->{'_line_length'} || $DEFAULTLINELEN;
}
=head2 tag_length
Title : tag_length
Usage : $obj->tag_length($newval)
Function:
Example : my $tag_length = $obj->tag_length
Returns : value of the length for each space-separated tag in a line
Args : newvalue (optional) - set to zero to have one tag per line
=cut
sub tag_length{
my ($self,$value) = @_;
if( defined $value) {
$self->{'_tag_length'} = $value;
}
return $self->{'_tag_length'} || $DEFAULTTAGLEN;
}
=head2 id_linebreak
Title : id_linebreak
Usage : $obj->id_linebreak($newval)
Function:
Returns : value of id_linebreak
Args : newvalue (optional)
=cut
sub id_linebreak{
my ($self,$value) = @_;
if( defined $value) {
$self->{'_id_linebreak'} = $value;
}
return $self->{'_id_linebreak'} || 0;
}
=head2 wrap_sequential
Title : wrap_sequential
Usage : $obj->wrap_sequential($newval)
Function:
Returns : value of wrap_sequential
Args : newvalue (optional)
=cut
sub wrap_sequential{
my ($self,$value) = @_;
if( defined $value) {
$self->{'_wrap_sequential'} = $value;
}
return $self->{'_wrap_sequential'} || 0;
}
=head2 longid
Title : longid
Usage : $obj->longid($newval)
Function:
Returns : value of longid
Args : newvalue (optional)
=cut
sub longid{
my ($self,$value) = @_;
if( defined $value) {
$self->{'_longid'} = $value;
}
return $self->{'_longid'} || 0;
}
1;