/usr/share/perl5/Bio/Tradis/Analysis/InsertSite.pm is in bio-tradis 1.3.3+dfsg-3.
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 | package Bio::Tradis::Analysis::InsertSite;
# ABSTRACT: Take in a bam file and plot the start position of each read
=head1 NAME
InsertSite.pm - Take in a bam file and plot the start position of each read
=head1 SYNOPSIS
Takes in a mapped BAM file and plot the start position of each read
use Bio::Tradis::Analysis::InsertSite;
my $insertsite_plots_from_bam = Bio::Tradis::Analysis::InsertSite->new(
filename => 'my_file.bam',
output_base_filename => 'my_output_file'
);
$insertsite_plots_from_bam->create_plots();
=cut
use Moose;
use Bio::Tradis::Parser::Bam;
use Bio::Tradis::Parser::Cigar;
has 'filename' => ( is => 'rw', isa => 'Str', required => 1 );
has 'output_base_filename' => ( is => 'rw', isa => 'Str', required => 1 );
has 'mapping_score' => ( is => 'ro', isa => 'Int', required => 1 );
has 'samtools_exec' => ( is => 'ro', isa => 'Str', default => 'samtools' );
has '_output_file_handles' => ( is => 'rw', isa => 'HashRef', lazy_build => 1 );
has '_sequence_names' => ( is => 'rw', isa => 'ArrayRef', lazy_build => 1 );
has '_sequence_base_counters' =>
( is => 'rw', isa => 'HashRef', lazy_build => 1 );
has '_sequence_information' =>
( is => 'rw', isa => 'HashRef', lazy_build => 1 );
has '_frequency_of_read_start' => (
is => 'rw',
isa => 'HashRef',
lazy => 1,
builder => '_build__frequency_of_read_start'
);
sub _build__sequence_information {
my ($self) = @_;
my %all_sequences_info =
Bio::Tradis::Parser::Bam->new( file => $self->filename, samtools_exec => $self->samtools_exec )->seq_info;
return \%all_sequences_info;
}
sub _build__sequence_names {
my ($self) = @_;
my @sequence_names = keys %{ $self->_sequence_information };
return \@sequence_names;
}
sub _build__sequence_base_counters {
my ($self) = @_;
my %sequence_base_counters;
for my $sequence_name ( @{ $self->_sequence_names } ) {
$sequence_base_counters{$sequence_name} = 0;
}
return \%sequence_base_counters;
}
sub _build__output_file_handles {
my ($self) = @_;
my $out = $self->output_base_filename;
chomp $out;
my %output_file_handles;
for my $sequence_name ( @{ $self->_sequence_names } ) {
my $file_sequence_name = $sequence_name;
$file_sequence_name =~ s/[^\w\d\.]/_/g;
my $cmd = "gzip > $out.$file_sequence_name.insert_site_plot.gz";
open( $output_file_handles{$sequence_name}, '|-', $cmd )
|| Bio::Tradis::Analysis::Exceptions::FailedToCreateOutputFileHandle
->throw( error =>
"Couldnt create output file handle for saving insertsite plot results for "
. $sequence_name . " in "
. $self->filename
. " and output base "
. $self->output_base_filename );
}
return \%output_file_handles;
}
sub _number_of_forward_reads {
my ( $self, $sequence_name, $read_coord ) = @_;
return $self->_number_of_reads( $sequence_name, $read_coord, 1 );
}
sub _number_of_reverse_reads {
my ( $self, $sequence_name, $read_coord ) = @_;
return $self->_number_of_reads( $sequence_name, $read_coord, -1 );
}
sub _number_of_reads {
my ( $self, $sequence_name, $read_coord, $direction ) = @_;
if (
defined(
$self->_frequency_of_read_start->{$sequence_name}{$read_coord}
)
&& defined(
$self->_frequency_of_read_start->{$sequence_name}{$read_coord}
{$direction}
)
)
{
return $self->_frequency_of_read_start->{$sequence_name}{$read_coord}
{$direction};
}
return 0;
}
# work out if padding is needed and return it as a formatted string
sub _create_padding_string {
my ( $self, $previous_counter, $current_counter ) = @_;
my $padding_string = "";
for ( my $i = $previous_counter + 1 ; $i < $current_counter ; $i++ ) {
$padding_string .= "0 0\n";
}
return $padding_string;
}
sub _print_padding_at_end_of_sequence {
my ($self) = @_;
for my $sequence_name ( @{ $self->_sequence_names } ) {
my $sequence_length =
$self->_sequence_information->{$sequence_name}->{'LN'};
next unless ( $sequence_length =~ /^[\d]+$/ );
$sequence_length++;
my $padding_string =
$self->_create_padding_string(
$self->_sequence_base_counters->{$sequence_name},
$sequence_length );
$self->_sequence_base_counters->{$sequence_name} = $sequence_length;
print { $self->_output_file_handles->{$sequence_name} } $padding_string;
}
}
sub _close_output_file_handles {
my ($self) = @_;
for my $output_file_handle ( values %{ $self->_output_file_handles } ) {
close($output_file_handle);
}
return;
}
sub _build__frequency_of_read_start {
my ($self) = @_;
my %frequency_of_read_start;
my $samtools_command = join(' ', ($self->samtools_exec, 'view', '-F', 4, '-q', $self->mapping_score, $self->filename));
open(my $samtools_view_fh,"-|" ,$samtools_command);
while(<$samtools_view_fh>)
{
my $sam_line = $_;
my @read_details = split("\t", $sam_line);
my $seqid = $read_details[2];
my $cigar_parser = Bio::Tradis::Parser::Cigar->new(cigar => $read_details[5], coordinate => $read_details[3]);
my $strand = 1;
$strand = -1 if(($read_details[1] & 0x10) == 0x10);
if ( $strand == 1 ) {
$frequency_of_read_start{$seqid}{ $cigar_parser->start }
{ $strand }++;
}
else {
$frequency_of_read_start{$seqid}{ $cigar_parser->end }
{ $strand }++;
}
}
return \%frequency_of_read_start;
}
sub create_plots {
my ($self) = @_;
my %read_starts = %{ $self->_frequency_of_read_start };
for my $sequence_name ( keys %read_starts ) {
my %sequence_read_coords = %{ $read_starts{$sequence_name} };
for my $read_coord ( sort { $a <=> $b } ( keys %sequence_read_coords ) )
{
my $padding_string =
$self->_create_padding_string(
$self->_sequence_base_counters->{$sequence_name}, $read_coord );
$self->_sequence_base_counters->{$sequence_name} = $read_coord;
my $forward_reads =
$self->_number_of_forward_reads( $sequence_name, $read_coord );
my $reverse_reads =
$self->_number_of_reverse_reads( $sequence_name, $read_coord );
print { $self->_output_file_handles->{$sequence_name} }
$padding_string . $forward_reads . " " . $reverse_reads . "\n";
}
}
$self->_print_padding_at_end_of_sequence;
$self->_close_output_file_handles;
return 1;
}
1;
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