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ktnyt/mztab_annotate.pl

Last active August 29, 2015 14:09
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mzTab Annotator - picks up "opt_global_kegg" column to automatically annotate SML lines
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mztab_annotate.pl
#!/usr/bin/env perl
###############################################################################
#
# Modules
#
use strict;
use warnings;
use utf8;
use POSIX;
use Encode;
use Storable;
use XML::Simple;
use JSON;
use LWP::Simple;
use LWP::UserAgent;
use URI::Escape;
use HTTP::Request::Common qw(POST);
use Mozilla::CA;
###############################################################################
###############################################################################
#
# Parse input
#
my %opts = (
force => 0,
help => 0,
input => "",
output => "",
verbose => 0
);
for(my $i = 0; $i < scalar(@ARGV); ++$i) {
if((my $name = $ARGV[$i]) =~ s/^--?//) {
if(exists($opts{$name})) {
my @value = ();
for(my $j = $i + 1; $j < scalar(@ARGV); ++$i, ++$j) {
if($ARGV[$j] =~ /^--?/) {
last;
}
push(@value, $ARGV[$j]);
}
if(@value) {
$opts{$name} = join(" ", @value);
} else {
$opts{$name} = 1;
}
}
}
}
if($opts{help} || !length($opts{input})) {
print_help(1);
}
###############################################################################
###############################################################################
#
# Read and parse input mzTab file
#
open my $ifh, "<", $opts{input} or die $!;
my $mztab;
while(my $line = <$ifh>) {
chomp($line);
if($line =~ /^(\w{3})/) {
push(@{$mztab->{$1}}, [split(/\t/, $line)]);
}
}
close $ifh;
###############################################################################
###############################################################################
#
# Annotation
#
my $keggcol = get_keggcol(@{$mztab->{SMH}->[0]});
my $inchicol = get_inchicol(@{$mztab->{SMH}->[0]});
my $smilescol = get_smilescol(@{$mztab->{SMH}->[0]});
my $formulacol = get_formulacol(@{$mztab->{SMH}->[0]});
my @kegg = map{$_->[$keggcol]}@{$mztab->{SML}};
my @map = kegg2map_array(@kegg);
my @brite = kegg2brite_array(@kegg);
my @drug = kegg2drug_array(@kegg);
my @disease = kegg2disease_array(@kegg);
my @chebi = kegg2chebi_array(@kegg);
my @chembl = kegg2chembl_array(@kegg);
my @metacyc = kegg2metacyc_array(@kegg);
my @uniquec = keggCompoundTraverse("B", @kegg);
my @uniquep = keggPathwayTraverse("B", @kegg);
my @inchi = chembl2inchi_array(@chembl);
my @smiles = chembl2smiles_array(@chembl);
my @formula = chembl2formula_array(@chembl);
push(@{$mztab->{SMH}->[0]}, "opt_global_chembl");
push(@{$mztab->{SMH}->[0]}, "opt_global_chebi");
push(@{$mztab->{SMH}->[0]}, "opt_global_metacyc");
push(@{$mztab->{SMH}->[0]}, "opt_global_kegg_pathway");
push(@{$mztab->{SMH}->[0]}, "opt_global_kegg_brite");
push(@{$mztab->{SMH}->[0]}, "opt_global_kegg_drug");
push(@{$mztab->{SMH}->[0]}, "opt_global_kegg_disease");
push(@{$mztab->{SMH}->[0]}, "opt_global_kegg_B");
push(@{$mztab->{SMH}->[0]}, "opt_global_kegg_pathway_B");
for(my $i = 0; $i < scalar(@{$mztab->{SML}}); ++$i) {
$mztab->{SML}->[$i]->[$inchicol] = $inchi[$i] if $inchicol;
$mztab->{SML}->[$i]->[$smilescol] = $smiles[$i] if $smilescol;
$mztab->{SML}->[$i]->[$formulacol] = $formula[$i] if $formulacol;
push(@{$mztab->{SML}->[$i]}, $chembl[$i]);
push(@{$mztab->{SML}->[$i]}, $chebi[$i]);
push(@{$mztab->{SML}->[$i]}, $metacyc[$i]);
push(@{$mztab->{SML}->[$i]}, $map[$i]);
push(@{$mztab->{SML}->[$i]}, $brite[$i]);
push(@{$mztab->{SML}->[$i]}, $drug[$i]);
push(@{$mztab->{SML}->[$i]}, $disease[$i]);
push(@{$mztab->{SML}->[$i]}, $uniquec[$i]);
push(@{$mztab->{SML}->[$i]}, $uniquep[$i]);
}
###############################################################################
###############################################################################
#
# Output in mzTab format
#
my $ofh = *STDOUT;
if(length($opts{output})) {
open($ofh, ">", $opts{output});
}
if(-e $opts{output}) {
if(!$opts{force}) {
printf(STDERR "Output file exists. Overwrite? [Y/n]: ");
if(<STDIN> !~ /y/i) {
printf(STDERR "Exiting...\n");
}
}
}
foreach my $section (qw(MTD SMH SML)) {
foreach my $line (@{$mztab->{$section}}) {
printf($ofh "%s\n", join("\t", @{$line}));
}
}
if(length($opts{output})) {
close $ofh;
}
###############################################################################
###############################################################################
#
# Subroutines
#
####################
# Parsing routines #
####################
sub get_keggcol {
my (@header) = (@_);
for(my $i = 0; $i < scalar(@header); ++$i) {
if($header[$i] eq "opt_global_kegg") {
return $i;
}
}
return 0;
}
sub get_inchicol {
my (@header) = (@_);
for(my $i = 0; $i < scalar(@header); ++$i) {
if($header[$i] eq "inchi_key") {
return $i;
}
}
return 0;
}
sub get_smilescol {
my (@header) = (@_);
for(my $i = 0; $i < scalar(@header); ++$i) {
if($header[$i] eq "smiles") {
return $i;
}
}
return 0;
}
sub get_formulacol {
my (@header) = (@_);
for(my $i = 0; $i < scalar(@header); ++$i) {
if($header[$i] eq "chemical_formula") {
return $i;
}
}
return 0;
}
#######################
# Annotation routines #
#######################
sub kegg2chembl_table {
my %table;
printf(STDERR "Creating kegg2chembl conversion table.\n") if $opts{verbose};
my $response = get("http://www.genome.jp/sparql/linkdb?default-graph-uri=http%3A%2F%2Flinkdb&query=BASE%20%3Chttp%3A%2F%2Fwww.genome.jp%2Flinkdb%2F%3E%0ASELECT%20%3Ffromlabel%20%3Ftolabel%20WHERE%20%7B%0A%3Ffrom%20%3Cequivalent%3E%20%3Fto%20.%0A%0A%3Ffrom%20%3Ccore%2Fdatabase%3E%20%3Ffromdb%20.%0A%3Fto%20%20%20%3Ccore%2Fdatabase%3E%20%3Ftodb%20.%0A%0A%3Ffromdb%20%3Ccore%2Fdblabel%3E%20%22compound%22%20.%0A%3Ftodb%20%20%20%3Ccore%2Fdblabel%3E%20%22chembl%22%20.%0A%0A%3Ffrom%20rdfs%3Alabel%20%3Ffromlabel%20.%0A%3Fto%20%20%20rdfs%3Alabel%20%3Ftolabel%20.%0A%7D%20ORDER%20BY%20%3Ffromlabel%20%3Ftolabel%0A&format=text/tab-separated-valuescs&timeout=0&debug=on");
foreach my $line (split(/\n/, $response)) {
my ($kegg, $chembl) = split(/\t/, $line);
if($kegg =~ s/".+:(.+)"/$1/g && $chembl =~ s/".+:(.+)"/$1/g) {
$table{$kegg} = $chembl;
}
}
printf(STDERR "Done.\n") if $opts{verbose};
return %table;
}
sub kegg2chembl_array {
my (@kegg) = (@_);
my %table = kegg2chembl_table();
return map{exists($table{$_}) ? $table{$_} : "null"}@kegg;
}
sub kegg2chebi_table {
my %table;
printf(STDERR "Creating kegg2chebi conversion table.\n") if $opts{verbose};
my $response = get("http://www.genome.jp/sparql/linkdb?default-graph-uri=http%3A%2F%2Flinkdb&query=BASE%20%3Chttp%3A%2F%2Fwww.genome.jp%2Flinkdb%2F%3E%0ASELECT%20%3Ffromlabel%20%3Ftolabel%20WHERE%20%7B%0A%3Ffrom%20%3Cequivalent%3E%20%3Fto%20.%0A%0A%3Ffrom%20%3Ccore%2Fdatabase%3E%20%3Ffromdb%20.%0A%3Fto%20%20%20%3Ccore%2Fdatabase%3E%20%3Ftodb%20.%0A%0A%3Ffromdb%20%3Ccore%2Fdblabel%3E%20%22compound%22%20.%0A%3Ftodb%20%20%20%3Ccore%2Fdblabel%3E%20%22chebi%22%20.%0A%0A%3Ffrom%20rdfs%3Alabel%20%3Ffromlabel%20.%0A%3Fto%20%20%20rdfs%3Alabel%20%3Ftolabel%20.%0A%7D%20ORDER%20BY%20%3Ffromlabel%20%3Ftolabel%0A&format=text/tab-separated-valuescs&timeout=0&debug=on");
foreach my $line (split(/\n/, $response)) {
my ($kegg, $chebi) = split(/\t/, $line);
if($kegg =~ s/".+:(.+)"/$1/g && $chebi =~ s/".+:(.+)"/$1/g) {
$table{$kegg} = $chebi;
}
}
printf(STDERR "Done.\n") if $opts{verbose};
return %table;
}
sub kegg2chebi_array {
my (@kegg) = (@_);
my %table = kegg2chebi_table();
return map{exists($table{$_}) ? $table{$_} : "null"}@kegg;
}
sub kegg2metacyc_table {
my (@kegg) = (@_);
my %table;
printf(STDERR "Creating kegg2metacyc conversion table.\n") if $opts{verbose};
my $url = sprintf("http://websvc.biocyc.org/ECOLI/foreignid?ids=%s", join(",", map{sprintf("Kegg:%s", $_)}@kegg));
my $response = get($url);
foreach my $line (split(/\n/, $response)) {
my ($kegg, $count, $metacyc) = split(/\t/, $line, 3);
$kegg =~ s/^Kegg://g;
if($count) {
$table{$kegg} = $metacyc;
}
}
printf(STDERR "Done.\n") if $opts{verbose};
return %table;
}
sub kegg2metacyc_array {
my (@kegg) = (@_);
my %table = kegg2metacyc_table(@kegg);
return map{exists($table{$_}) ? $table{$_} : "null"}@kegg;
}
sub kegg2map_table {
my %table;
printf(STDERR "Creating kegg2map conversion table.\n") if $opts{verbose};
my $response = get("http://rest.kegg.jp/link/pathway/compound");
foreach my $line (split(/\n/, $response)) {
if($line =~ /cpd:(C\d+)\tpath:(map\d+)/) {
my ($kegg, $map) = ($1, $2);
push(@{$table{$kegg}}, $map);
}
}
foreach my $kegg (keys %table) {
$table{$kegg} = sprintf("%s", join(",", @{$table{$kegg}}));
}
printf(STDERR "Done.\n") if $opts{verbose};
return %table;
}
sub kegg2map_array {
my (@kegg) = (@_);
my %table = kegg2map_table();
return map{exists($table{$_}) ? $table{$_} : "null"}@kegg;
}
sub kegg2drug_table {
my %table;
printf(STDERR "Creating kegg2drug conversion table.\n") if $opts{verbose};
my $response = get("http://rest.kegg.jp/link/drug/compound");
foreach my $line (split(/\n/, $response)) {
if($line =~ /cpd:(C\d+)\tdr:(D\d+)/) {
my ($kegg, $drug) = ($1, $2);
push(@{$table{$kegg}}, $drug);
}
}
foreach my $kegg (keys %table) {
$table{$kegg} = sprintf("%s", join(",", @{$table{$kegg}}));
}
printf(STDERR "Done.\n") if $opts{verbose};
return %table;
}
sub kegg2drug_array {
my (@kegg) = (@_);
my %table = kegg2drug_table();
return map{exists($table{$_}) ? $table{$_} : "null"}@kegg;
}
sub kegg2disease_table {
my %table;
printf(STDERR "Creating kegg2disease conversion table.\n") if $opts{verbose};
my $response = get("http://rest.kegg.jp/link/disease/compound");
foreach my $line (split(/\n/, $response)) {
if($line =~ /cpd:(C\d+)\tds:(H\d+)/) {
my ($kegg, $disease) = ($1, $2);
push(@{$table{$kegg}}, $disease);
}
}
foreach my $kegg (keys %table) {
$table{$kegg} = sprintf("%s", join(",", @{$table{$kegg}}));
}
printf(STDERR "Done.\n") if $opts{verbose};
return %table;
}
sub kegg2disease_array {
my (@kegg) = (@_);
my %table = kegg2disease_table();
return map{exists($table{$_}) ? $table{$_} : "null"}@kegg;
}
sub kegg2brite_table {
my %table;
printf(STDERR "Creating kegg2brite conversion table.\n") if $opts{verbose};
my $response = get("http://rest.kegg.jp/link/brite/compound");
foreach my $line (split(/\n/, $response)) {
if($line =~ /cpd:(C\d+)\tbr:(br\d+)/) {
my ($kegg, $brite) = ($1, $2);
push(@{$table{$kegg}}, $brite);
}
}
foreach my $kegg (keys %table) {
$table{$kegg} = sprintf("%s", join(",", @{$table{$kegg}}));
}
printf(STDERR "Done.\n") if $opts{verbose};
return %table;
}
sub kegg2brite_array {
my (@kegg) = (@_);
my %table = kegg2brite_table();
return map{exists($table{$_}) ? $table{$_} : "null"}@kegg;
}
sub keggCompoundTraverse_table {
my $text = get("http://rest.kegg.jp/get/br:br08001");
sleep(2);
my $table;
my ($cA, $cB, $cC);
foreach my $line (split(/[\r\n]/, $text)) {
if(my ($level, $category) = ($line =~ /^([ABCD]) *(.+)$/)) {
if($level eq "A") {
$category =~ s/ *\[.+\]$//g;
$cA = $category;
} elsif($level eq "B") {
$category =~ s/ *\[.+\]$//g;
$cB = $category;
} elsif($level eq "C") {
$category =~ s/ *\[.+\]$//g;
$cC = $category;
} else {
my ($kegg, $name) = split(/\s/, $category);
$table->{$kegg}->{A} = $cA;
$table->{$kegg}->{B} = $cB;
$table->{$kegg}->{C} = $cC;
}
}
}
return $table;
}
sub keggCompoundTraverse {
my ($level, @kegg) = (@_);
my $table = keggCompoundTraverse_table();
return map{exists($table->{$_}->{$level}) ? $table->{$_}->{$level}: "null"}@kegg;
}
sub keggPathwayTraverse_table {
my $text = get("http://rest.kegg.jp/get/br:br08901");
sleep(2);
my $table;
my @Bterms;
my ($cA, $cB);
my %k2m = kegg2map_table();
foreach my $line (split(/[\r\n]/, $text)) {
if(my ($level, $category) = ($line =~ /^([ABC]) *(.+)$/)) {
if($level eq "A") {
$cA = $category;
} elsif($level eq "B") {
push(@Bterms, $category);
$cB = $category;
} else {
my ($map, $name) = split(/\s/, $category);
$table->{"map$map"}->{A} = $cA;
$table->{"map$map"}->{B} = $cB;
}
}
}
my $ret;
foreach my $kegg (keys(%k2m)) {
foreach my $level (qw(A B)) {
my $tmp;
foreach my $map (split(/,/, $k2m{$kegg})) {
$tmp->{$table->{$map}->{$level}}++;
}
my @order = map{$_->[0]}sort{$b->[1] <=> $a->[1]}map{[$_, $tmp->{$_}]}keys(%{$tmp});
$ret->{$kegg}->{$level} = $order[0];
}
}
return $ret;
}
sub keggPathwayTraverse {
my ($level, @kegg) = (@_);
my $table = keggPathwayTraverse_table();
return map{exists($table->{$_}->{$level}) ? $table->{$_}->{$level}: "null"}@kegg;
}
sub chembl2inchi_table {
my (@chembl) = grep{!/null/}(@_);
printf(STDERR "Creating chembl2inchi conversion table.\n") if $opts{verbose};
my %table;
my $n = 200;
my $max = ceil(scalar(@chembl) / $n);
for (my $i = 0; $i * $n < scalar(@chembl); ++$i) {
sleep(2) if $i;
printf(STDERR "\r\e[KBatch %d out of %d (%.3f %%)", $i + 1, $max , (($i + 1) / $max) * 100) if $opts{verbose};
my $query_template = <<EOQ;
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX cco: <http://rdf.ebi.ac.uk/terms/chembl#>
SELECT ?id ?key
WHERE {
\%s
}
ORDER BY ?label
EOQ
my $union_template = <<EOT;
\{
<http://rdf.ebi.ac.uk/resource/chembl/molecule/\%s> cco:chemblId ?id .
<http://rdf.ebi.ac.uk/resource/chembl/molecule/\%s#standard_inchi_key> <http://semanticscience.org/resource/SIO_000300> ?key .
\}
EOT
my $offset = $i * $n;
my $remain = scalar(@chembl) - $offset;
my $limit = $remain > $n ? $n : $remain;
my $union = join("UNION\n", map{sprintf($union_template, $_, $_)}@chembl[$offset..($offset+$limit-1)]);
my $query = sprintf($query_template, $union);
my $endpoint = "https://www.ebi.ac.uk/rdf/services/chembl/servlet/query";
my %params = (
query => $query,
offset => 0,
limit => $limit,
inference => "false"
);
my $request = POST($endpoint, [%params]);
my $ua = LWP::UserAgent->new();
$ua->ssl_opts( SSL_ca_file => Mozilla::CA::SSL_ca_file() );
my $response = $ua->request($request);
my $ref = XMLin($response->content());
foreach my $result (map{$_->{binding}}@{$ref->{results}->{result}}) {
my $id = $result->{id}->{literal};
my $key = $result->{key}->{literal};
$table{$id} = $key;
}
}
printf(STDERR "\nDone.\n") if $opts{verbose};
return %table;
}
sub chembl2inchi_array {
my (@chembl) = (@_);
my %table = chembl2inchi_table(@chembl);
return map{exists($table{$_}) ? $table{$_} : "null"}@chembl;
}
sub chembl2smiles_table {
my (@chembl) = grep{!/null/}(@_);
printf(STDERR "Creating chembl2smiles conversion table.\n") if $opts{verbose};
my %table;
my $n = 200;
my $max = ceil(scalar(@chembl) / $n);
for (my $i = 0; $i * $n < scalar(@chembl); ++$i) {
sleep(2) if $i;
printf(STDERR "\r\e[KBatch %d out of %d (%.3f %%)", $i + 1, $max , (($i + 1) / $max) * 100) if $opts{verbose};
my $query_template = <<EOQ;
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX cco: <http://rdf.ebi.ac.uk/terms/chembl#>
SELECT ?id ?key
WHERE {
\%s
}
ORDER BY ?label
EOQ
my $union_template = <<EOT;
\{
<http://rdf.ebi.ac.uk/resource/chembl/molecule/\%s> cco:chemblId ?id .
<http://rdf.ebi.ac.uk/resource/chembl/molecule/\%s#canonical_smiles> <http://semanticscience.org/resource/SIO_000300> ?key .
\}
EOT
my $offset = $i * $n;
my $remain = scalar(@chembl) - $offset;
my $limit = $remain > $n ? $n : $remain;
my $union = join("UNION\n", map{sprintf($union_template, $_, $_)}@chembl[$offset..($offset+$limit-1)]);
my $query = sprintf($query_template, $union);
my $endpoint = "https://www.ebi.ac.uk/rdf/services/chembl/servlet/query";
my %params = (
query => $query,
offset => 0,
limit => $limit,
inference => "false"
);
my $request = POST($endpoint, [%params]);
my $ua = LWP::UserAgent->new();
$ua->ssl_opts( SSL_ca_file => Mozilla::CA::SSL_ca_file() );
my $response = $ua->request($request);
my $ref = XMLin($response->content());
foreach my $result (map{$_->{binding}}@{$ref->{results}->{result}}) {
my $id = $result->{id}->{literal};
my $key = $result->{key}->{literal};
$table{$id} = $key;
}
}
printf(STDERR "\nDone.\n") if $opts{verbose};
return %table;
}
sub chembl2smiles_array {
my (@chembl) = (@_);
my %table = chembl2smiles_table(@chembl);
return map{exists($table{$_}) ? $table{$_} : "null"}@chembl;
}
sub chembl2formula_table {
my (@chembl) = grep{!/null/}(@_);
printf(STDERR "Creating chembl2formula conversion table.\n") if $opts{verbose};
my %table;
my $n = 200;
my $max = ceil(scalar(@chembl) / $n);
for (my $i = 0; $i * $n < scalar(@chembl); ++$i) {
sleep(2) if $i;
printf(STDERR "\r\e[KBatch %d out of %d (%.3f %%)", $i + 1, $max , (($i + 1) / $max) * 100) if $opts{verbose};
my $query_template = <<EOQ;
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX cco: <http://rdf.ebi.ac.uk/terms/chembl#>
SELECT ?id ?key
WHERE {
\%s
}
ORDER BY ?label
EOQ
my $union_template = <<EOT;
\{
<http://rdf.ebi.ac.uk/resource/chembl/molecule/\%s> cco:chemblId ?id .
<http://rdf.ebi.ac.uk/resource/chembl/molecule/\%s#full_molformula> <http://semanticscience.org/resource/SIO_000300> ?key .
\}
EOT
my $offset = $i * $n;
my $remain = scalar(@chembl) - $offset;
my $limit = $remain > $n ? $n : $remain;
my $union = join("UNION\n", map{sprintf($union_template, $_, $_)}@chembl[$offset..($offset+$limit-1)]);
my $query = sprintf($query_template, $union);
my $endpoint = "https://www.ebi.ac.uk/rdf/services/chembl/servlet/query";
my %params = (
query => $query,
offset => 0,
limit => $limit,
inference => "false"
);
my $request = POST($endpoint, [%params]);
my $ua = LWP::UserAgent->new();
$ua->ssl_opts( SSL_ca_file => Mozilla::CA::SSL_ca_file() );
my $response = $ua->request($request);
my $ref = XMLin($response->content());
foreach my $result (map{$_->{binding}}@{$ref->{results}->{result}}) {
my $id = $result->{id}->{literal};
my $key = $result->{key}->{literal};
$table{$id} = $key;
}
}
printf(STDERR "\nDone.\n") if $opts{verbose};
return %table;
}
sub chembl2formula_array {
my (@chembl) = (@_);
my %table = chembl2formula_table(@chembl);
return map{exists($table{$_}) ? $table{$_} : "null"}@chembl;
}
##########################
# Miscellaneous routines #
##########################
sub print_help {
print <<EOS;
mztab_annotate.pl - Annotate mztab file according to provided metadata
Usage:
perl mztab_annotate.pl [options] [--input] <input> [--output] <output>
Options:
--force Force overwrite the input file.
--input Input mzTab file.
--output Name of mzTab output file. Defaults to STDOUT.
--verbose Execute in verbose mode.
EOS
my $status = shift || 0;
exit($status);
}
###############################################################################
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