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POD syntax fixes
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svn path=/bioperl-run/branches/branch-07/; revision=12940
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@heikkil
heikkil committed Mar 3, 2001
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109 changes: 57 additions & 52 deletions Bio/Tools/Run/Alignment/Clustalw.pm
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Expand Up @@ -11,28 +11,32 @@


=head1 NAME =head1 NAME
Bio::Tools::Run::Alignment::Clustalw - Object for the calculation of a multiple sequence alignment Bio::Tools::Run::Alignment::Clustalw - Object for the calculation of a
from a set of unaligned sequences or alignments using the Clustalw program multiple sequence alignment from a set of unaligned sequences or
alignments using the Clustalw program
=head1 SYNOPSIS =head1 SYNOPSIS
# Build a clustalw alignment factory # Build a clustalw alignment factory
@params = ('ktuple' => 2, 'matrix' => 'BLOSUM'); @params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
$factory = Bio::Tools::Run::Alignment::Clustalw->new(@params); $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
# Pass the factory a list of sequences to be aligned. # Pass the factory a list of sequences to be aligned.
$inputfilename = 't/cysprot.fa'; $inputfilename = 't/cysprot.fa';
$aln = $factory->align($inputfilename); # $aln is a SimpleAlign object. $aln = $factory->align($inputfilename); # $aln is a SimpleAlign object.
or # or
$seq_array_ref = \@seq_array; # where @seq_array is an array of Bio::Seq objects $seq_array_ref = \@seq_array;
$aln = $factory->align($seq_array_ref); # where @seq_array is an array of Bio::Seq objects
$aln = $factory->align($seq_array_ref);
# Or one can pass the factory a pair of (sub)alignments to be aligned against each other, e.g.: # Or one can pass the factory a pair of (sub)alignments
$aln = $factory->profile_align($aln1,$aln2); # where $aln1 and $aln2 are Bio::SimpleAlign objects. #to be aligned against each other, e.g.:
$aln = $factory->profile_align($aln1,$aln2);
# where $aln1 and $aln2 are Bio::SimpleAlign objects.
# Or one can pass the factory an alignment and one or more unaligned # Or one can pass the factory an alignment and one or more unaligned
# sequences to be added to the alignment. For example: # sequences to be added to the alignment. For example:
$aln = $factory->profile_align($aln1,$seq); # $seq is a Bio::Seq object. $aln = $factory->profile_align($aln1,$seq); # $seq is a Bio::Seq object.
There are various additional options and input formats available. See There are various additional options and input formats available. See
the DESCRIPTION section that follows for additional details. the DESCRIPTION section that follows for additional details.
Expand Down Expand Up @@ -106,7 +110,7 @@ alignment to an initial alignment.
Input to align() may consist of a set of unaligned sequences in the Input to align() may consist of a set of unaligned sequences in the
form of the name of file containing the sequences. For example, form of the name of file containing the sequences. For example,
$inputfilename = 't/cysprot.fa'; $aln = $inputfilename = 't/cysprot.fa'; $aln =
$factory->align($inputfilename); $factory-E<gt>align($inputfilename);
Alternately one can create an array of Bio::Seq objects somehow Alternately one can create an array of Bio::Seq objects somehow
Expand Down Expand Up @@ -170,42 +174,42 @@ me know.
These can be specified as paramters when instantiating a new TCoffee These can be specified as paramters when instantiating a new TCoffee
object, or through get/set methods of the same name (lowercase). object, or through get/set methods of the same name (lowercase).
=head2 PARAMETER FOR ALIGNMENT COMPUTATION =head1 PARAMETER FOR ALIGNMENT COMPUTATION
=head2 KTUPLE =head2 KTUPLE
Title : KTUPLE Title : KTUPLE
Description : (optional) set the word size to be used in the alignment Description : (optional) set the word size to be used in the alignment
This is the size of exactly matching fragment that is used. This is the size of exactly matching fragment that is used.
INCREASE for speed (max= 2 for proteins; 4 for DNA), INCREASE for speed (max= 2 for proteins; 4 for DNA),
DECREASE for sensitivity. DECREASE for sensitivity.
For longer sequences (e.g. >1000 residues) you may For longer sequences (e.g. >1000 residues) you may
need to increase the default need to increase the default
=head2 TOPDIAGS =head2 TOPDIAGS
Title : TOPDIAGS Title : TOPDIAGS
Description : (optional) number of best diagonals to use Description : (optional) number of best diagonals to use
The number of k-tuple matches on each diagonal The number of k-tuple matches on each diagonal
(in an imaginary dot-matrix plot) is calculated. (in an imaginary dot-matrix plot) is calculated.
Only the best ones (with most matches) are used in Only the best ones (with most matches) are used in
the alignment. This parameter specifies how many. the alignment. This parameter specifies how many.
Decrease for speed; increase for sensitivity. Decrease for speed; increase for sensitivity.
=head2 WINDOW =head2 WINDOW
Title : WINDOW Title : WINDOW
Description : (optional) window size Description : (optional) window size
This is the number of diagonals around each of the 'best' This is the number of diagonals around each of the 'best'
diagonals that will be used. Decrease for speed; diagonals that will be used. Decrease for speed;
increase for sensitivity. increase for sensitivity.
=head2 PAIRGAP =head2 PAIRGAP
Title : PAIRGAP Title : PAIRGAP
Description : (optional) gap penalty for pairwise alignments Description : (optional) gap penalty for pairwise alignments
This is a penalty for each gap in the fast alignments. This is a penalty for each gap in the fast alignments.
It has little affect on the speed or sensitivity except It has little affect on the speed or sensitivity except
for extreme values. for extreme values.
=head2 FIXEDGAP =head2 FIXEDGAP
Expand All @@ -220,8 +224,8 @@ object, or through get/set methods of the same name (lowercase).
=head2 MATRIX =head2 MATRIX
Title : MATRIX Title : MATRIX
Default : PAM100 for DNA - PAM250 for protein alignment Default : PAM100 for DNA - PAM250 for protein alignment
Description : (optional) substitution matrix used in the multiple Description : (optional) substitution matrix used in the multiple
alignments. Depends on the version of clustalw as to alignments. Depends on the version of clustalw as to
what default matrix will be used what default matrix will be used
Expand Down Expand Up @@ -301,13 +305,13 @@ The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _ methods. Internal methods are usually preceded with a _
=cut =cut
#'


#'


package Bio::Tools::Run::Alignment::Clustalw; package Bio::Tools::Run::Alignment::Clustalw;


use vars qw($AUTOLOAD @ISA $DEBUG $PROGRAM $PROGRAMDIR use vars qw($AUTOLOAD @ISA $DEBUG $PROGRAM $PROGRAMDIR
$TMPDIR $TMPOUTFILE @CLUSTALW_SWITCHES @CLUSTALW_PARAMS $TMPDIR $TMPOUTFILE @CLUSTALW_SWITCHES @CLUSTALW_PARAMS
@OTHER_SWITCHES %OK_FIELD); @OTHER_SWITCHES %OK_FIELD);
use strict; use strict;
use Bio::Seq; use Bio::Seq;
Expand All @@ -322,17 +326,17 @@ use Bio::Root::IO;
BEGIN { BEGIN {


# You will need to enable Clustalw to find the clustalw program. This # You will need to enable Clustalw to find the clustalw program. This
# can be done in (at least) three ways: # can be done in (at least) three ways:


# 1. Modify your $PATH variable to include your clustalw directory as # 1. Modify your $PATH variable to include your clustalw directory as
# in (for Linux): # in (for Linux):
# export PATH=$PATH:/home/peter/clustalw1.8 # export PATH=$PATH:/home/peter/clustalw1.8
# #
# 2. define an environmental variable CLUSTALDIR: # 2. define an environmental variable CLUSTALDIR:
# export CLUSTALDIR=/home/peter/clustalw1.8 # export CLUSTALDIR=/home/peter/clustalw1.8
# #
# 3. include a definition of an environmental variable CLUSTALDIR in # 3. include a definition of an environmental variable CLUSTALDIR in
# every script that will use Clustal.pm. # every script that will use Clustal.pm.
# $ENV{CLUSTALDIR} = '/home/peter/clustalw1.8/'; # $ENV{CLUSTALDIR} = '/home/peter/clustalw1.8/';


$PROGRAMDIR = $ENV{CLUSTALDIR} || ''; $PROGRAMDIR = $ENV{CLUSTALDIR} || '';
Expand All @@ -350,7 +354,7 @@ BEGIN {


@OTHER_SWITCHES = qw(QUIET); @OTHER_SWITCHES = qw(QUIET);
# Authorize attribute fields # Authorize attribute fields
foreach my $attr ( @CLUSTALW_PARAMS, @CLUSTALW_SWITCHES, foreach my $attr ( @CLUSTALW_PARAMS, @CLUSTALW_SWITCHES,
@OTHER_SWITCHES ) { $OK_FIELD{$attr}++; } @OTHER_SWITCHES ) { $OK_FIELD{$attr}++; }




Expand All @@ -363,14 +367,14 @@ sub new {
unless (&exists_clustal()) { unless (&exists_clustal()) {
warn "Clustalw program not found as $PROGRAM or not executable. \n Clustalw can be obtained from eg- http://corba.ebi.ac.uk/Biocatalog/Alignment_Search_software.html/ \n"; warn "Clustalw program not found as $PROGRAM or not executable. \n Clustalw can be obtained from eg- http://corba.ebi.ac.uk/Biocatalog/Alignment_Search_software.html/ \n";
} }

my ($attr, $value); my ($attr, $value);
(undef,$TMPDIR) = $self->tempdir(CLEANUP=>1); (undef,$TMPDIR) = $self->tempdir(CLEANUP=>1);
(undef,$TMPOUTFILE) = $self->tempfile(-dir => $TMPDIR); (undef,$TMPOUTFILE) = $self->tempfile(-dir => $TMPDIR);
while (@args) { while (@args) {
$attr = shift @args; $attr = shift @args;
$value = shift @args; $value = shift @args;
next if( $attr =~ /^-/ ); # don't want named parameters next if( $attr =~ /^-/ ); # don't want named parameters
$self->$attr($value); $self->$attr($value);
} }
return $self; return $self;
Expand Down Expand Up @@ -415,7 +419,7 @@ or
$aln = $factory->align($seq_array_ref); $aln = $factory->align($seq_array_ref);
Function: Perform a multiple sequence alignment Function: Perform a multiple sequence alignment
Example : Example :
Returns : Reference to a SimpleAlign object containing the Returns : Reference to a SimpleAlign object containing the
sequence alignment. sequence alignment.
Args : Name of a file containing a set of unaligned fasta sequences Args : Name of a file containing a set of unaligned fasta sequences
or else an array of references to Bio::Seq objects. or else an array of references to Bio::Seq objects.
Expand Down Expand Up @@ -478,7 +482,7 @@ sub profile_align {
my $param_string = $self->_setparams(); my $param_string = $self->_setparams();


# run clustalw # run clustalw
my $aln = $self->_run('profile-aln', $infilename1, my $aln = $self->_run('profile-aln', $infilename1,
$infilename2, $param_string); $infilename2, $param_string);


} }
Expand All @@ -490,13 +494,14 @@ sub profile_align {
Usage : Internal function, not to be called directly Usage : Internal function, not to be called directly
Function: makes actual system call to clustalw program Function: makes actual system call to clustalw program
Example : Example :
Returns : nothing; clustalw output is written to a Returns : nothing; clustalw output is written to a
temporary file $TMPOUTFILE temporary file $TMPOUTFILE
Args : Name of a file containing a set of unaligned fasta sequences Args : Name of a file containing a set of unaligned fasta sequences
and hash of parameters to be passed to clustalw and hash of parameters to be passed to clustalw
=cut =cut

sub _run { sub _run {
my ($self,$command,$infile1,$infile2,$param_string) = @_; my ($self,$command,$infile1,$infile2,$param_string) = @_;
my $instring; my $instring;
Expand Down Expand Up @@ -526,9 +531,9 @@ sub _run {
# Clean up the temporary files created along the way... # Clean up the temporary files created along the way...
# Replace file suffix with dnd to find name of dendrogram file(s) to delete # Replace file suffix with dnd to find name of dendrogram file(s) to delete
foreach my $f ( $infile1, $infile2 ) { foreach my $f ( $infile1, $infile2 ) {
$f =~ s/\.[^\.]*$// ; $f =~ s/\.[^\.]*$// ;
unlink $f .'.dnd' if( $f ne '' ); unlink $f .'.dnd' if( $f ne '' );
} }
return $aln; return $aln;
} }


Expand Down Expand Up @@ -565,12 +570,12 @@ sub _setinput {
if (ref($input) eq "ARRAY") { if (ref($input) eq "ARRAY") {
# Open temporary file for both reading & writing of BioSeq array # Open temporary file for both reading & writing of BioSeq array
($tfh,$infilename) = $self->tempfile(-dir=>$TMPDIR); ($tfh,$infilename) = $self->tempfile(-dir=>$TMPDIR);
$temp = Bio::SeqIO->new('-fh'=>$tfh, $temp = Bio::SeqIO->new('-fh'=>$tfh,
'-format' =>'Fasta'); '-format' =>'Fasta');


# Need at least 2 seqs for alignment # Need at least 2 seqs for alignment
unless (scalar(@$input) > 1) {return 0;} unless (scalar(@$input) > 1) {return 0;}

foreach $seq (@$input) { foreach $seq (@$input) {
unless (ref($seq) eq "Bio::Seq") unless (ref($seq) eq "Bio::Seq")
{return 0;} {return 0;}
Expand Down Expand Up @@ -608,7 +613,7 @@ sub _setinput {
Usage : Internal function, not to be called directly Usage : Internal function, not to be called directly
Function: Create parameter inputs for clustalw program Function: Create parameter inputs for clustalw program
Example : Example :
Returns : parameter string to be passed to clustalw Returns : parameter string to be passed to clustalw
during align or profile_align during align or profile_align
Args : name of calling object Args : name of calling object
Expand Down

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