/usr/lib/x86_64-linux-gnu/perl5/5.20/TFBS/Run/ConservationProfileGenerator.pm is in libtfbs-perl 0.6.1+dfsg-1+b1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 | package TFBS::Run::ConservationProfileGenerator;
use strict;
use Bio::Root::Root;
use TFBS::ConservationProfile;
use Bio::AlignIO;
use constant DEFAULT_WINDOW => 50;
use constant DEFAULT_CUTOFF => 0.7;
use vars qw'@ISA';
@ISA = qw'Bio::Root::Root';
sub new {
my ( $caller, %args ) = @_;
my $self = bless {
alignment => undef,
ref_sequence => undef,
method => undef,
window => DEFAULT_WINDOW,
cutoff => DEFAULT_CUTOFF,
%args
},
ref $caller || $caller;
if ( !defined( $self->alignment )
or !$self->alignment->isa("Bio::SimpleAlign") )
{
$self->throw( "alignment: argument missing or wrong object type: "
. ref( $self->alignment ) );
}
return $self;
}
sub run {
my ( $self, %args ) = @_;
my $method = ( $args{method} or $self->method or "simple" );
my %method_subref = (
simple => \&_run_simple,
malin => \&_run_Malins,
align_cons => \&_run_align_cons
);
if ( !defined( $method_subref{$method} ) ) {
$self->throw("method $method not supported");
}
$method_subref{$method}->( $self, %args );
}
sub alignment {
$_[0]->{'alignment'};
}
sub ref_sequence {
$_[0]->{'ref_sequence'};
}
sub method {
$_[0]->{'method'};
}
sub window {
$_[0]->{'window'};
}
sub cutoff {
$_[0]->{'cutoff'};
}
sub _run_simple {
my ( $self, %args ) = @_;
my ( $window_size, $cutoff, $ref_seq_nr, $other_seq_nr ) =
$self->_rearrange( [qw(WINDOW CUTOFF REF_SEQ_NR OTHER_SEQ_NR)], %args );
$window_size = $self->window unless $window_size;
$cutoff = $self->cutoff unless $cutoff;
$ref_seq_nr = 1 if !$ref_seq_nr;
$other_seq_nr = ( $other_seq_nr or 3 - $ref_seq_nr );
my @seq1 = split "", $self->alignment->get_seq_by_pos($ref_seq_nr)->seq;
my @seq2 = split "", $self->alignment->get_seq_by_pos($other_seq_nr)->seq;
my @CONSERVATION;
my @match;
while ( $seq1[0] eq "-" or $seq1[0] eq "." ) {
shift @seq1;
shift @seq2;
}
for my $i ( 0 .. $#seq1 ) {
push( @match, ( uc( $seq1[$i] ) eq uc( $seq2[$i] ) ? 1 : 0 ) )
unless ( $seq1[$i] eq "-" or $seq1[$i] eq "." );
}
my @graph = ( $match[0] );
for my $i ( 1 .. ( $#match + $window_size / 2 ) ) {
$graph[$i] = $graph[ $i - 1 ] + ( $i > $#match ? 0 : $match[$i] ) -
( $i < $window_size ? 0 : $match[ $i - $window_size ] );
}
# at this point, the graph values are shifted $window_size/2 to the right
# i.e. the score at a certain position is the score of the window
# UPSTREAM of it: To fix it, we shoud discard the first $window_size/2 scores:
#$self->conservation1 ([]);
foreach my $match_point ( @graph[ int( $window_size / 2 ) .. $#graph ] ) {
push @CONSERVATION, $match_point / $window_size;
}
return TFBS::ConservationProfile->new(
conservation => \@CONSERVATION,
parameters => {
window => $window_size,
cutoff => $cutoff,
ref_seq_nr => $ref_seq_nr,
other_seq_nr => $other_seq_nr,
method => "simple"
},
ref_sequence => $self->ref_sequence,
alignment => $self->alignment
);
}
sub _run_Malins {
shift->throw(
"Not implemeted, sorry. Pick another method for the time being");
}
sub _run_align_cons {
my ( $self, %args ) = @_;
my ( $window_size, $increment, $cutoff, $stringency, $format, $prog ) =
$self->_rearrange(
[qw(WINDOW INCREMENT CUTOFF STRINGENCY FORMAT PROGRAM)], %args );
my %params = (
-w => $window_size,
-n => $increment,
-t => $cutoff,
-s => $stringency,
-r => "p",
-f => ( $format or "c" ) # center by default
);
$prog = "align_cons" unless defined $prog;
my @cl_args;
while ( my ( $param, $value ) = each %params ) {
if ( defined $value ) {
push @cl_args, $param, $value;
}
}
my $alnstring = $self->_alignment_to_string("fasta");
$alnstring =~ s/[\"\$]/\\$1/gs; # escape things that might confuse echo
my $command = join " ", $prog, @cl_args;
my @output_lines = `echo "$alnstring" | $command`;
# add error checking here!!!
my @CONSERVATION;
foreach my $line (@output_lines) {
chomp $line;
$line =~ s/^\D+//;
my ( $pos, $value ) = split /\s+/, $line;
push @CONSERVATION, $value;
}
return TFBS::ConservationProfile->new(
conservation => \@CONSERVATION,
parameters => {
window => $window_size,
cutoff => $cutoff,
increment => $increment,
stringency => $stringency,
method => "align_cons"
},
alignment => $self->alignment,
ref_sequence => $self->ref_sequence
);
}
sub _alignment_to_string {
my ( $self, $format ) = ( @_, "fasta" );
my $alnstring;
my $fh = IO::String->new($alnstring);
my $outstream = Bio::AlignIO->new( -fh => $fh, -format => $format );
$outstream->write_aln( $self->alignment );
$outstream->close;
return $alnstring;
}
#sub _UNIT_TESTS {
# require Test;
# require CONSNP::Test::TestObjects;
# my $to = CONSNP::Test::TestObjects->new;
#
# plan(tests => 5);
#
# exit(0);
#
#
#}
1;
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