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Add --db-index, --db-file, --taxonomy, --db-pipe for piped db files #89

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Add --db-index, --db-file, --taxonomy, --db-pipe for piped db files #89

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146 changes: 86 additions & 60 deletions scripts/kraken
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Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,12 @@ my $min_hits = 1;
my $fasta_input = 0;
my $fastq_input = 0;
my $db_prefix;
my $idx_file;
my $kdb_file;
my $db_size;
my $idx_size;
my $db_pipe = 0;
my $taxonomy;
my $threads;
my $preload = 0;
my $gunzip = 0;
Expand All @@ -55,7 +61,7 @@ my $check_names = 0;
my $only_classified_output = 0;
my $unclassified_out;
my $classified_out;
my $outfile;
my @outfiles;

GetOptions(
"help" => \&display_help,
Expand All @@ -64,11 +70,17 @@ GetOptions(
"threads=i" => \$threads,
"fasta-input" => \$fasta_input,
"fastq-input" => \$fastq_input,
"db-index=s" => \$idx_file,
"db-file=s" => \$kdb_file,
"db-size=i" => \$db_size,
"index-size=i" => \$idx_size,
"db-pipe" => \$db_pipe,
"taxonomy=s" => \$taxonomy,
"quick" => \$quick,
"min-hits=i" => \$min_hits,
"unclassified-out=s" => \$unclassified_out,
"classified-out=s" => \$classified_out,
"output=s" => \$outfile,
"output=s" => \@outfiles,
"preload" => \$preload,
"paired" => \$paired,
"check-names" => \$check_names,
Expand All @@ -85,31 +97,41 @@ if (! @ARGV) {
print STDERR "Need to specify input filenames!\n";
usage();
}
eval { $db_prefix = krakenlib::find_db($db_prefix); };
if ($@) {
die "$PROG: $@";

if (!defined $kdb_file || !defined $idx_file || !defined $taxonomy) {
eval { $db_prefix = krakenlib::find_db($db_prefix); };
if ($@) {
die "$PROG: $@";
}
}

my $taxonomy = "$db_prefix/taxonomy/nodes.dmp";
if (!defined $taxonomy) {
$taxonomy = "$db_prefix/taxonomy/nodes.dmp";
}
if ($quick) {
undef $taxonomy; # Skip loading nodes file, not needed in quick mode
undef $taxonomy; # Skip loading nodes file, not needed in quick mode
}

my $kdb_file = "$db_prefix/database.kdb";
my $idx_file = "$db_prefix/database.idx";
if (! -e $kdb_file) {
die "$PROG: $kdb_file does not exist!\n";
if (!defined $kdb_file) {
$kdb_file = "$db_prefix/database.kdb";
if (! -e $kdb_file) {
die "$PROG: $kdb_file does not exist!\n";
}
}
if (! -e $idx_file) {
die "$PROG: $idx_file does not exist!\n";

if (!defined $idx_file) {
$idx_file = "$db_prefix/database.idx";
if (! -e $idx_file) {
die "$PROG: $idx_file does not exist!\n";
}
}

if ($min_hits > 1 && ! $quick) {
die "$PROG: --min_hits requires --quick to be specified\n";
}

if ($paired && @ARGV != 2) {
die "$PROG: --paired requires exactly two filenames\n";
if ($paired && scalar @ARGV % 2 ) {
die "$PROG: --paired requires 2x filenames\n";
}

my $compressed = $gunzip || $bunzip2;
Expand All @@ -135,65 +157,64 @@ if ($auto_detect) {
my @flags;
push @flags, "-d", $kdb_file;
push @flags, "-i", $idx_file;
push @flags, "-D", $db_size if defined $db_size;
push @flags, "-I", $idx_size if defined $idx_size;
push @flags, "-t", $threads if $threads > 1;
push @flags, "-n", $taxonomy if defined $taxonomy;
push @flags, "-q" if $quick;
push @flags, "-p" if $db_pipe;
push @flags, "-m", $min_hits if $min_hits > 1;
push @flags, "-f" if $fastq_input && ! $paired; # merger always outputs FASTA
push @flags, "-U", $unclassified_out if defined $unclassified_out;
push @flags, "-C", $classified_out if defined $classified_out;
push @flags, "-o", $outfile if defined $outfile;
if (@outfiles) {
foreach my $outfile (@outfiles) {
push @flags, "-o", $outfile;
}
}
push @flags, "-c", if $only_classified_output;
push @flags, "-M" if $preload;

# handle piping for decompression/merging
my @pipe_argv;
if ($paired) {
my @merge_flags;
push @merge_flags, "--fa" if $fasta_input;
push @merge_flags, "--fq" if $fastq_input;
push @merge_flags, "--gz" if $gunzip;
push @merge_flags, "--bz2" if $bunzip2;
push @merge_flags, "--check-names" if $check_names;
@pipe_argv = ("read_merger.pl", @merge_flags, @ARGV);
}
elsif ($compressed) {
if ($gunzip) {
@pipe_argv = ("gzip", "-dc", @ARGV);
}
elsif ($bunzip2) {
@pipe_argv = ("bzip2", "-dc", @ARGV);
}
else {
die "$PROG: unrecognized compression program! This is a Kraken bug.\n";
}
}
my @pipe_argvv;
foreach (my $i = 0; $i < @ARGV; $i++) {
my @pipe_argv;
my $use_pipe = 0;
if ($paired) {
$use_pipe = 1;

my @merge_flags;
push @merge_flags, "--fa" if $fasta_input;
push @merge_flags, "--fq" if $fastq_input;
push @merge_flags, "--gz" if $gunzip;
push @merge_flags, "--bz2" if $bunzip2;
push @merge_flags, "--check-names" if $check_names;
@pipe_argv = ("read_merger.pl", @merge_flags, @ARGV[$i, $i+1]);
$i++;
}
elsif ($compressed) {
$use_pipe = 1;

if ($gunzip) {
@pipe_argv = ("gzip", "-dc", $ARGV[$i]);
}
elsif ($bunzip2) {
@pipe_argv = ("bzip2", "-dc", $ARGV[$i]);
}
else {
die "$PROG: unrecognized compression program! This is a Kraken bug.\n";
}
} else {
@pipe_argv = $ARGV[$i];
}
if ($use_pipe) {
@pipe_argv = ( "<(", @pipe_argv, ")" );
}
push @pipe_argvv, @pipe_argv;

# if args exist, set up the pipe/fork/exec
if (@pipe_argv) {
pipe RD, WR;
my $pid = fork();
if ($pid < 0) {
die "$PROG: fork error: $!\n";
}
if ($pid) {
open STDIN, "<&RD"
or die "$PROG: can't dup stdin to read end of pipe: $!\n";
close RD;
close WR;
@ARGV = ("/dev/fd/0"); # make classifier read from pipe
}
else {
open STDOUT, ">&WR"
or die "$PROG: can't dup stdout to write end of pipe: $!\n";
close RD;
close WR;
exec @pipe_argv
or die "$PROG: can't exec $pipe_argv[0]: $!\n";
}
}

exec $CLASSIFY, @flags, @ARGV;
exec join(" ", ("exec /bin/bash -c \"exec", $CLASSIFY, @flags, @pipe_argvv, "\""));
die "$PROG: exec error: $!\n";

sub usage {
Expand All @@ -212,6 +233,11 @@ Options:
--fastq-input Input is FASTQ format
--gzip-compressed Input is gzip compressed
--bzip2-compressed Input is bzip2 compressed
--db-index Path for db index file
--db-file Path for db file
--db-size Size of db file
--index-size Size of db index file
--db-pipe DB is piped
--quick Quick operation (use first hit or hits)
--min-hits NUM In quick op., number of hits req'd for classification
NOTE: this is ignored if --quick is not specified
Expand Down
6 changes: 3 additions & 3 deletions scripts/read_merger.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -47,9 +47,9 @@
for my $file (@ARGV) {
if (! -e $file) {
die "$PROG: $file does not exist\n";
}
if (! -f $file) {
die "$PROG: $file is not a regular file\n";
}
if (! (-f $file || -p $file)) {
die "$PROG: $file is not a file or pipe\n";
}
}

Expand Down
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