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Adding per-sequence name translation
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,147 @@ | ||
| #!/usr/bin/perl | ||
|
|
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| # Copyright 2013-2015, Derrick Wood <[email protected]> | ||
| # | ||
| # This file is part of the Kraken taxonomic sequence classification system. | ||
| # | ||
| # Kraken is free software: you can redistribute it and/or modify | ||
| # it under the terms of the GNU General Public License as published by | ||
| # the Free Software Foundation, either version 3 of the License, or | ||
| # (at your option) any later version. | ||
| # | ||
| # Kraken is distributed in the hope that it will be useful, | ||
| # but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| # GNU General Public License for more details. | ||
| # | ||
| # You should have received a copy of the GNU General Public License | ||
| # along with Kraken. If not, see <http://www.gnu.org/licenses/>. | ||
|
|
||
| # For each classified read, prints sequence ID and full taxonomy | ||
|
|
||
| use strict; | ||
| use warnings; | ||
| use File::Basename; | ||
| use Getopt::Long; | ||
|
|
||
| my $PROG = basename $0; | ||
| my $KRAKEN_DIR = "#####=KRAKEN_DIR=#####"; | ||
|
|
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| # Test to see if the executables got moved, try to recover if we can | ||
| if (! -e "$KRAKEN_DIR/classify") { | ||
| use Cwd 'abs_path'; | ||
| $KRAKEN_DIR = dirname abs_path($0); | ||
| } | ||
|
|
||
| require "$KRAKEN_DIR/krakenlib.pm"; | ||
|
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| my $db_prefix; | ||
| my $mpa_format = 0; | ||
|
|
||
| GetOptions( | ||
| "help" => \&display_help, | ||
| "version" => \&display_version, | ||
| "db=s" => \$db_prefix, | ||
| "mpa-format" => \$mpa_format | ||
| ); | ||
|
|
||
| eval { $db_prefix = krakenlib::find_db($db_prefix); }; | ||
| if ($@) { | ||
| die "$PROG: $@"; | ||
| } | ||
|
|
||
| sub display_help { | ||
| print STDERR "Usage: $PROG [--db KRAKEN_DB_NAME] <kraken output file(s)>\n"; | ||
| exit 0; | ||
| } | ||
|
|
||
| sub display_version { | ||
| print "Kraken version #####=VERSION=#####\n"; | ||
| print "Copyright 2013-2015, Derrick Wood (dwood\@cs.jhu.edu)\n"; | ||
| exit 0; | ||
| } | ||
|
|
||
| my (%parent_map, %name_map, %rank_map); | ||
| load_taxonomy($db_prefix); | ||
| my %known_taxonomy_strings; | ||
|
|
||
| while (<>) { | ||
| next unless /^C/; | ||
| chomp; | ||
| my @fields = split; | ||
| my ($seqid, $taxid) = @fields[1,2]; | ||
| my $taxonomy_str = get_taxonomy_str($taxid); | ||
| print "$seqid\t$taxonomy_str\n"; | ||
| } | ||
|
|
||
| sub get_taxonomy_str { | ||
| my $taxid = shift; | ||
| if (! exists $known_taxonomy_strings{$taxid}) { | ||
| my @nodes; | ||
| while ($taxid > 0) { | ||
| if ($mpa_format) { | ||
| my $rank_code = rank_code($rank_map{$taxid}); | ||
| my $name = $name_map{$taxid}; | ||
| $name =~ tr/ /_/; | ||
| unshift @nodes, lc($rank_code) . "__" . $name if $rank_code ne "-"; | ||
| } | ||
| else { | ||
| unshift @nodes, $name_map{$taxid}; | ||
| } | ||
| $taxid = $parent_map{$taxid}; | ||
| } | ||
| if ($mpa_format) { | ||
| $known_taxonomy_strings{$taxid} = @nodes ? join("|", @nodes) : "root"; | ||
| } | ||
| else { | ||
| $known_taxonomy_strings{$taxid} = join(";", @nodes); | ||
| } | ||
| } | ||
| return $known_taxonomy_strings{$taxid}; | ||
| } | ||
|
|
||
| sub rank_code { | ||
| my $rank = shift; | ||
| for ($rank) { | ||
| $_ eq "species" and return "S"; | ||
| $_ eq "genus" and return "G"; | ||
| $_ eq "family" and return "F"; | ||
| $_ eq "order" and return "O"; | ||
| $_ eq "class" and return "C"; | ||
| $_ eq "phylum" and return "P"; | ||
| $_ eq "kingdom" and return "K"; | ||
| $_ eq "superkingdom" and return "D"; | ||
| } | ||
| return "-"; | ||
| } | ||
|
|
||
| sub load_taxonomy { | ||
| my $prefix = shift; | ||
|
|
||
| open NAMES, "<", "$prefix/taxonomy/names.dmp" | ||
| or die "$PROG: can't open names file: $!\n"; | ||
| while (<NAMES>) { | ||
| chomp; | ||
| s/\t\|$//; | ||
| my @fields = split /\t\|\t/; | ||
| my ($node_id, $name, $type) = @fields[0,1,3]; | ||
| if ($type eq "scientific name") { | ||
| $name_map{$node_id} = $name; | ||
| } | ||
| } | ||
| close NAMES; | ||
|
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| open NODES, "<", "$prefix/taxonomy/nodes.dmp" | ||
| or die "$PROG: can't open nodes file: $!\n"; | ||
| while (<NODES>) { | ||
| chomp; | ||
| my @fields = split /\t\|\t/; | ||
| my ($node_id, $parent_id, $rank) = @fields[0,1,2]; | ||
| if ($node_id == 1) { | ||
| $parent_id = 0; | ||
| } | ||
| $parent_map{$node_id} = $parent_id; | ||
| $rank_map{$node_id} = $rank; | ||
| } | ||
| close NODES; | ||
| } |