Bio::AlignIO phylip
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Summary
Bio::AlignIO::phylip - PHYLIP format sequence input/output stream
Package variables
No package variables defined.
Included modules
Bio::SimpleAlign
POSIX
Inherit
Bio::AlignIO
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); }
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 => 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 =>
1. ID strings can be surrounded by single quoted. They are mandatory
only if the IDs contain spaces.
Methods
BEGIN Code
_initialize
No description
Code
next_alnDescriptionCode
write_alnDescriptionCode
interleavedDescriptionCode
flag_SIDescriptionCode
idlengthDescriptionCode
line_lengthDescriptionCode
tag_lengthDescriptionCode
id_linebreakDescriptionCode
wrap_sequentialDescriptionCode
longidDescriptionCode
Methods description
next_alncode    nextTop
 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 : Bio::SimpleAlign object
Args :
write_alncodeprevnextTop
 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 : Bio::Align::AlignI object
interleavedcodeprevnextTop
 Title   : interleaved
Usage : my $interleaved = $obj->interleaved
Function: Get/Set Interleaved status
Returns : boolean
Args : boolean
flag_SIcodeprevnextTop
 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
idlengthcodeprevnextTop
 Title   : idlength
Usage : my $idlength = $obj->idlength
Function: Get/Set value of id length
Returns : string
Args : string
line_lengthcodeprevnextTop
 Title   : line_length
Usage : $obj->line_length($newval)
Function:
Returns : value of line_length
Args : newvalue (optional)
tag_lengthcodeprevnextTop
 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
id_linebreakcodeprevnextTop
 Title   : id_linebreak
Usage : $obj->id_linebreak($newval)
Function:
Returns : value of id_linebreak
Args : newvalue (optional)
wrap_sequentialcodeprevnextTop
 Title   : wrap_sequential
Usage : $obj->wrap_sequential($newval)
Function:
Returns : value of wrap_sequential
Args : newvalue (optional)
longidcodeprevnextTop
 Title   : longid
Usage : $obj->longid($newval)
Function:
Returns : value of longid
Args : newvalue (optional)
Methods code
BEGINTop
BEGIN {
    $DEFAULTIDLENGTH = 10;
    $DEFAULTLINELEN = 60;
    $DEFAULTTAGLEN = 10;
}
_initializedescriptionprevnextTop
sub _initialize {
  my($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;
}
next_alndescriptionprevnextTop
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 $aln;
}
write_alndescriptionprevnextTop
sub write_aln {
    my ($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 $self->_fh; return 1;
}
interleaveddescriptionprevnextTop
sub interleaved {
   my ($self,$value) = @_;
   if( defined $value ) {
       if ($value) {$self->{'_interleaved'} = 1 }
       else {$self->{'_interleaved'} = 0 }
   }
   return 1 unless defined $self->{'_interleaved'};
   return $self->{'_interleaved'};
}
flag_SIdescriptionprevnextTop
sub flag_SI {
   my ($self,$value) = @_;
   my $previous = $self->{'_flag_SI'};
   if( defined $value ) {
       $self->{'_flag_SI'} = $value;
   }
   return $previous;
}
idlengthdescriptionprevnextTop
sub idlength {
	my($self,$value) = @_;
	if (defined $value){
	   $self->{'_idlength'} = $value;
	}
	return $self->{'_idlength'};
}
line_lengthdescriptionprevnextTop
sub line_length {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'_line_length'} = $value;
    }
    return $self->{'_line_length'} || $DEFAULTLINELEN;
}
tag_lengthdescriptionprevnextTop
sub tag_length {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'_tag_length'} = $value;
    }
    return $self->{'_tag_length'} || $DEFAULTTAGLEN;
}
id_linebreakdescriptionprevnextTop
sub id_linebreak {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'_id_linebreak'} = $value;
    }
    return $self->{'_id_linebreak'} || 0;
}
wrap_sequentialdescriptionprevnextTop
sub wrap_sequential {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'_wrap_sequential'} = $value;
    }
    return $self->{'_wrap_sequential'} || 0;
}
longiddescriptionprevnextTop
sub longid {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'_longid'} = $value;
    }
    return $self->{'_longid'} || 0;
}

1;
}
General documentation
FEEDBACKTop
SupportTop
Please direct usage questions or support issues to the mailing list:
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.
Reporting BugsTop
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/
AUTHORS - Heikki Lehvaslaiho and Jason StajichTop
Email: heikki at ebi.ac.uk
Email: jason at bioperl.org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
newTop
 Title   : new
Usage : my $alignio = Bio::AlignIO->new(-format => 'phylip'
-file => '>file',
-idlength => 10,
-idlinebreak => 1);
Function: Initialize a new Bio::AlignIO::phylip reader or writer
Returns : 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)