new parser for miRBase xrefs, replaces use of ncRNA_DBParser in ensembl

misc-scripts/xref_mapping/XrefParser/miRBaseParser.pm

+package XrefParser::miRBaseParser;
+
+use strict;
+use warnings;
+use Carp;
+use DBI;
+
+use base qw(XrefParser::BaseParser);
+
+
+sub run {
+
+  my ($self, $ref_arg) = @_;
+  my $source_id    = $ref_arg->{source_id};
+  my $species_id   = $ref_arg->{species_id};
+  my $files        = $ref_arg->{files};
+  my $verbose      = $ref_arg->{verbose};
+
+  if((!defined $source_id) or (!defined $species_id) or (!defined $files) ){
+    croak "Need to pass source_id, species_id and files as pairs";
+  }
+  $verbose |=0;
+
+  my $file = @{$files}[0];
+
+  if(!defined($species_id)){
+    $species_id = $self->get_species_id_for_filename($file);
+  }
+
+  my $xrefs = $self->create_xrefs($source_id, $file, $species_id);
+  if(!defined($xrefs)){
+    return 1; #error
+  }
+  # upload
+  if(!defined($self->upload_xref_object_graphs($xrefs))){
+    return 1; 
+  }
+  return 0; # successfull
+
+}
+
+# --------------------------------------------------------------------------------
+# Parse file into array of xref objects
+
+sub create_xrefs {
+
+  my ($self, $source_id, $file, $species_id) = @_;
+
+  my %species2name = $self->species_id2name();
+  my @names   = @{$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
+    $sequence =~ s/[\d+,\s+]//g;
+
+#    print "$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;
+
+}
+
+
+1;