Raw content of XrefParser::UniGeneParser
<![CDATA[# Parse UniGene Hs.seq.uniq files to create xrefs.
package XrefParser::UniGeneParser;
use strict;
use File::Basename;
use base qw( XrefParser::BaseParser );
my $verbose;
# --------------------------------------------------------------------------------
# Parse command line and run if being run directly
if (!defined(caller())) {
if (scalar(@ARGV) != 1) {
print "\nUsage: UniGeneParser.pm file.SPC <source_id> <species_id>\n\n";
exit(1);
}
run($ARGV[0], -1);
}
# --------------------------------------------------------------------------------
sub run {
my $self = shift if (defined(caller(1)));
my $source_id = shift;
my $species_id = shift;
my $files = shift;
my $release_file = shift;
$verbose = shift;
my $uniq_file = @{$files}[0];
my $data_file = @{$files}[1];
my $unigene_source_id = $self->get_source_id_for_source_name('UniGene');
print "UniGene source ID = $unigene_source_id.\n" if($verbose);
if ( !defined($species_id) ) {
$species_id =
$self->get_species_id_for_filename($uniq_file);
}
my $xrefs =
$self->create_xrefs( $unigene_source_id, $unigene_source_id,
$uniq_file, $data_file, $species_id );
if(!defined($xrefs)){
return 1; #error
}
if(!defined($self->upload_xref_object_graphs($xrefs))){
return 1; # error
}
if ( defined $release_file ) {
# Get species name from species ID.
my $species_name;
my $sth =
$self->dbi()
->prepare("SELECT name FROM species WHERE species_id = ?");
$sth->execute($species_id);
$sth->bind_columns( \$species_name );
$sth->fetchrow_array();
$species_name =~ tr/_/ /;
# Parse and set release info.
my $release;
my $release_io = $self->get_filehandle($release_file);
while ( defined( my $line = $release_io->getline() ) ) {
if ( $line =~ /^(.*$species_name)/i ) {
$release = $1;
}
}
$release_io->close();
if ( defined $release ) {
$release =~ s/\s{2,}/ /g;
$release =~ s/^(.*) UniGene/$1, UniGene/;
print "UniGene release: '$release'\n" if($verbose);
$self->set_release( $unigene_source_id, $release );
}
}
return 0; # successfull
}
my %geneid_2_desc;
sub get_desc{
my $self = shift;
my $data_file = shift;
my $dir = dirname($data_file);
local $/ = "//";
my $desc_io = $self->get_filehandle( $data_file );
if ( !defined $desc_io ) {
print STDERR "ERROR: Can't open $data_file\n";
return undef;
}
while ( $_ = $desc_io->getline() ) {
#ID Hs.159356
#TITLE Hypothetical LOC388277
(my $id) = $_ =~ /ID\s+(\S+)/;
(my $descrip) = $_ =~ /TITLE\s+(.+)\n/;
if ( defined $id && defined $descrip ) {
$geneid_2_desc{$id} = $descrip;
}
}
$desc_io->close();
return 1;
}
sub create_xrefs {
my $self = shift;
my ( $peptide_source_id, $unigene_source_id, $uniq_file, $data_file,
$species_id )
= @_;
# Create a hash of all valid names for this species. Not used...
# my %species2name = $self->species_id2name();
# my @names = @{$species2name{$species_id}};
# my %name2species_id = map{ $_=>$species_id } @names;
if ( !defined( $self->get_desc($data_file) ) ) {
return undef;
}
my $unigene_io = $self->get_filehandle($uniq_file);
if ( !defined $unigene_io ) {
print STDERR "Can't open RefSeq file $uniq_file\n";
return undef;
}
#>gnl|UG|Hs#S19185843 Homo sapiens N-acetyltransferase 2 (arylamine N-acetyltransferase)
# , mRNA (cDNA clone MGC:71963 IMAGE:4722596), complete cds /cds=(105,977) /gb=BC067218 /gi=45501306 /ug=Hs.2 /len=1344
#GGGGACTTCCCTTGCAGACTTTGGAAGGGAGAGCACTTTATTACAGACCTTGGAAGCAAG
my @xrefs;
local $/ = "\n>";
while ( $_ = $unigene_io->getline() ) {
my $xref;
my $entry = $_;
chomp $entry;
my ($header, $sequence) = split (/\n/, $entry, 2);
$sequence =~ s/^>//;
# remove newlines
my @seq_lines = split (/\n/, $sequence);
$sequence = join("", @seq_lines);
# (my $gnl, my $n, my $rest) = split(/\|/, $header,3);
(my $acc_no_ver) = $header =~ /\/ug=(\S*)/;
if(!defined($geneid_2_desc{$acc_no_ver})){
print "****$_\n";
$geneid_2_desc{$acc_no_ver} = "";
warn "No desc for $acc_no_ver\n";
}
$xref->{SEQUENCE_TYPE} = 'dna';
$xref->{STATUS} = 'experimental';
$xref->{SOURCE_ID} = $unigene_source_id;
##No species check as files contain data fro only one species.
$xref->{ACCESSION} = $acc_no_ver;
$xref->{LABEL} = $acc_no_ver;
$xref->{DESCRIPTION} = $geneid_2_desc{$acc_no_ver};
$xref->{SEQUENCE} = $sequence;
$xref->{SPECIES_ID} = $species_id;
$xref->{INFO_TYPE} = "SEQUENCE_MATCH";
push @xrefs, $xref;
}
$unigene_io->close();
%geneid_2_desc=();
print "Read " . scalar(@xrefs) ." xrefs from $uniq_file\n" if($verbose);
return \@xrefs;
}
1;
]]>