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package FastaIndex;
use strict;
use warnings;
use IO::File;
BEGIN {
for my $field (qw( fastaFileName startpos lines fh ))
{
my $slot = __PACKAGE__ . "::$field";
no strict "refs"; # So symbolic ref to typeglob works.
*$field = sub
{
my $self = shift;
$self->{$slot} = shift if @_;
return $self->{$slot};
};
}
}
sub new {
my ($this) = @_;
my $class = ref($this) || $this;
my $self = {};
bless $self, $class;
return $self;
}
sub make_index {
my ($this, $fastaFileName, $idregex, $dbmFileName) = @_;
if(!defined $idregex) { $idregex = "(\\S+)"; }
$this->fastaFileName($fastaFileName);
#open(IN, "$fastaFileName") or die "could not open $fastaFileName";
my $in = IO::File->new("$fastaFileName") or die "could not open $fastaFileName";
$this->fh($in);
if($dbmFileName)
{
my %openpos = ();
dbmopen( %openpos, $dbmFileName.".pos", 0666) || die ("Could not open DBM file $dbmFileName.pos");
$this->startpos(\%openpos);
my %openlines = ();
dbmopen( %openlines, $dbmFileName.".lines", 0666) || die ("Could not open DBM file $dbmFileName.lines");
$this->lines(\%openlines);
my $sizepos = scalar keys %openpos;
my $sizelines = scalar keys %openlines;
if($sizepos != $sizelines) { die "DBM files broken $dbmFileName\n"; }
if($sizepos > 0) {
print STDERR ("Index file $dbmFileName.pos already exists; assuming valid\n");
return;
};
}
else
{
# just store a hash in memory.
$this->startpos({});
$this->lines({});
}
my $lastpos = 0;
my $pos = 0;
#my $seq = "";
my $id = "";
my $numlines = 0;
while(<$in>)
{
my $line = $_;
if($line =~ /^>$idregex/)
{
if(defined $id && $id ne "") {
# write the previous record
#print STDERR "$id -> $lastpos\n";
$this->startpos()->{$id} = $lastpos;
$this->lines()->{$id} = $numlines;
}
# start a new record
$id = $1;
#$seq = $line;
$lastpos = $pos;
$numlines = 0;
}
# else { $seq .= $line; }
$pos += length($line);
$numlines++;
}
# write the final record
$this->startpos()->{$id} = $lastpos;
$this->lines()->{$id} = $numlines;
#delete($this->startpos()->{""}); # spurious entries from the start of the loop
#delete($this->lines()->{""}); # spurious entries from the start of the loop
}
sub count_records()
{
my ($this) = @_;
return scalar(keys %{$this->startpos()});
}
sub fetch {
my ($this, $id) = @_;
my $pos = $this->startpos()->{$id};
if(! defined $pos) { die "no sequence with id: $id in " . $this->fastaFileName(); }
my $numlines = $this->lines()->{$id};
my $result = "";
my $in = $this->fh();
#print $this->fastaFileName() . ": " . $in . "\n";
seek($in,$pos,0);
for (1..$numlines) { $result .= <$in> }
return $result;
}
sub close {
my ($this) = @_;
my $in = $this->fh();
close($in);
$this->startpos(undef);
$this->lines(undef);
}
1;
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