my ($self, $source_id, $file, $species_id, $dbi, $species_name) = @_;
my %species2name = $self->species_id2name($dbi);
if (defined $species_name) { push @{$species2name{$species_id}}, $species_name; }
if (!defined $species2name{$species_id}) { next; }
my @names = @{$species2name{$species_id}};
my %name2species_id =
map{ $_=>$species_id } @names;
my $file_io = $self->get_filehandle($file);
if ( !defined $file_io ) {
print STDERR "ERROR: Could not open $file\n";
return 1; # 1 is an error
}
my @xrefs;
local $/ = "\n\/\/";
while ($_ = $file_io->getline()) {
my $xref;
my $entry = $_;
chomp $entry;
next if (!$entry);
my ($header, $sequence) = split (/\nSQ/, $entry, 2);
# remove newlines
my @seq_lines = split (/\n/, $sequence) if ($sequence);
# drop the information line
shift @seq_lines;
# put onto one line
$sequence = join("", @seq_lines);
# make uppercase
$sequence = uc($sequence);
# replace Ts for Us
$sequence =~ s/U/T/g;
# remove numbers and whitespace
$sequence =~ s/[\d+,\s+]
# print "$header\n";
my ($name) = $header =~ /\nID\s+(\S+)\s+/;
my ($acc) = $header =~ /\nAC\s+(\S+);\s+/;
my ($description) = $header =~ /\nDE\s+(.+)\s+stem-loop/;
my @description_parts = split (/\s+/, $description) if ($description);
# remove the miRNA identifier
pop @description_parts;
my $species = join(" ", @description_parts);
$xref->{SEQUENCE_TYPE} = 'dna';
$xref->{STATUS} = 'experimental';
$xref->{SOURCE_ID} = $source_id;
$species = lc $species;
$species =~ s/ /_/;
my $species_id_check = $name2species_id{$species};
next if (!defined($species_id_check));
# skip xrefs for species that aren't in the species table
if (defined($species_id) and $species_id == $species_id_check) {
$xref->{ACCESSION} = $acc;
$xref->{LABEL} = $name;
$xref->{DESCRIPTION} = $name;
$xref->{SEQUENCE} = $sequence;
$xref->{SPECIES_ID} = $species_id;
# TODO synonyms, dependent xrefs etc
push @xrefs, $xref;
}
}
$file_io->close();
print "Read " . scalar(@xrefs) ." xrefs from $file\n";
return \@xrefs;
}
Code:
