Format the result of diamond (vs.nr) xml file for blast2go

diamond2b2g.pl

#!/usr/bin/perl

=head1 SCRIPT NAME

diamond2b2g.pl

=head1 DESCRIPTION

Format the result of diamond (vs.nr) xml file for blast2go

=head1 USAGE
0. Run diamond
 $ diamond blastx --db nr --out result.xml --query query.fa --outfmt 5
 
1. Make GI and accession list
 $ blastdbcmd -db nr -entry all -outfmt "%g %i" > gilist
 $ head gilist
  489223532 ref|WP_003131952.1|
  15674171 ref|NP_268346.1|
  13878750 sp|Q9CDN0.1|RS18_LACLA

2. Run
 $ perl diamond2b2g.pl gilistdb result.xml > result_forb2g.xml

=cut

#!/usr/bin/perl

$gilist = $ARGV[0];
$diamondxml = $ARGV[1];

open G, $gilist;
while(<G>) {
  @a = split;
  $a[1] =~ /^(\w+)\|([\w\.]+)/;
  $db = $1;
  $acc = $2;
  $hash{$acc} = "$a[0]\t$db";
}
close G;

open D, $diamondxml;
while(<D>) {
  if (/<Hit_id>([\w\.\-]+)</) {
    $acc = $1;
    @gidb = split("\t", $hash{$acc});
    $gi = $gidb[0];
    $db = $gidb[1];
    print "<Hit_id>gi|$gi|$db|$acc|</Hit_id>\n";
  }
  else {
    print;
  }
}

close D;