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emboss_cons.pl
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#!/usr/bin/env perl
=head1 NAME
emboss_cons.pl
=head1 DESCRIPTION
EMBOSS cons (REST) web service Perl client using L<LWP>.
Tested with:
=over
=item *
L<LWP> 6.35, L<XML::Simple> 2.25 and Perl 5.22.0 (MacOS 10.13.6)
=back
For further information see:
=over
=item *
L<https://www.ebi.ac.uk/Tools/webservices/>
=back
=head1 LICENSE
Copyright 2012-2024 EMBL - European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
Perl Client Automatically generated with:
https://github.com/ebi-jdispatcher/webservice-clients-generator
=cut
# ======================================================================
# Enable Perl warnings
use strict;
use warnings;
# Load libraries
use English;
use LWP;
use XML::Simple;
use Getopt::Long qw(:config no_ignore_case bundling);
use File::Basename;
use Data::Dumper;
use Time::HiRes qw(usleep);
# Base URL for service
my $baseUrl = 'https://www.ebi.ac.uk/Tools/services/rest/emboss_cons';
my $version = '2024-07-12 11:05';
# Set interval for checking status
my $checkInterval = 3;
# Set maximum number of 'ERROR' status calls to call job failed.
my $maxErrorStatusCount = 3;
# Output level
my $outputLevel = 1;
# Process command-line options
my $numOpts = scalar(@ARGV);
my %params = (
'debugLevel' => 0,
'maxJobs' => 1
);
# Default parameter values (should get these from the service)
GetOptions(
# Tool specific options
'sequence=s' => \$params{'sequence'}, # Sequence similarity search result (e.g. BLAST or FASTA search report) or a multiple sequence alignment.
'plurality=s' => \$params{'plurality'}, # Cut-off for the number of positive matches below which there is no consensus.
'setcase=s' => \$params{'setcase'}, # The threshold for the positive matches above which the consensus is in upper-case and below which the consensus is in lower-case.
'name=s' => \$params{'name'}, # Name of the consensus sequence.
'identity=i' => \$params{'identity'}, # The required number of identities at a site for it to give a consensus at that position.
'matrix=s' => \$params{'matrix'}, # Default substitution scoring matrices.
'stype=s' => \$params{'stype'}, # Defines the type of the sequences to be aligned
# Generic options
'email=s' => \$params{'email'}, # User e-mail address
'title=s' => \$params{'title'}, # Job title
'outfile=s' => \$params{'outfile'}, # Output file name
'outformat=s' => \$params{'outformat'}, # Output file type
'jobid=s' => \$params{'jobid'}, # JobId
'help|h' => \$params{'help'}, # Usage help
'asyncjob' => \$params{'asyncjob'}, # Asynchronous submission
'polljob' => \$params{'polljob'}, # Get results
'pollFreq=f' => \$params{'pollFreq'}, # Poll Frequency
'resultTypes' => \$params{'resultTypes'}, # Get result types
'status' => \$params{'status'}, # Get status
'params' => \$params{'params'}, # List input parameters
'paramDetail=s' => \$params{'paramDetail'}, # Get details for parameter
'verbose' => \$params{'verbose'}, # Increase output level
'version' => \$params{'version'}, # Prints out the version of the Client and exit.
'quiet' => \$params{'quiet'}, # Decrease output level
'debugLevel=i' => \$params{'debugLevel'}, # Debugging level
'baseUrl=s' => \$baseUrl, # Base URL for service.
);
if ($params{'verbose'}) {$outputLevel++}
if ($params{'quiet'}) {$outputLevel--}
if ($params{'pollFreq'}) {$checkInterval = $params{'pollFreq'} * 1000 * 1000}
if ($params{'baseUrl'}) {$baseUrl = $params{'baseUrl'}}
# Debug mode: LWP version
&print_debug_message('MAIN', 'LWP::VERSION: ' . $LWP::VERSION,
1);
# Debug mode: print the input parameters
&print_debug_message('MAIN', "params:\n" . Dumper(\%params), 11);
# LWP UserAgent for making HTTP calls (initialised when required).
my $ua;
# Get the script filename for use in usage messages
my $scriptName = basename($0, ());
# Print usage and exit if requested
if ($params{'help'} || $numOpts == 0) {
&usage();
exit(0);
}
# Debug mode: show the base URL
&print_debug_message('MAIN', 'baseUrl: ' . $baseUrl, 1);
if (
!(
$params{'polljob'}
|| $params{'resultTypes'}
|| $params{'status'}
|| $params{'params'}
|| $params{'paramDetail'}
|| $params{'version'}
)
&& !(defined($ARGV[0]) || defined($params{'sequence'}))
) {
# Bad argument combination, so print error message and usage
print STDERR 'Error: bad option combination', "\n";
&usage();
exit(1);
}
# Get parameters list
elsif ($params{'params'}) {
&print_tool_params();
}
# Get parameter details
elsif ($params{'paramDetail'}) {
&print_param_details($params{'paramDetail'});
}
# Print Client version
elsif ($params{'version'}) {
print STDOUT 'Revision: ' . $version, "\n";
exit(1);
}
# Job status
elsif ($params{'status'} && defined($params{'jobid'})) {
&print_job_status($params{'jobid'});
}
# Result types
elsif ($params{'resultTypes'} && defined($params{'jobid'})) {
&print_result_types($params{'jobid'});
}
# Poll job and get results
elsif ($params{'polljob'} && defined($params{'jobid'})) {
&get_results($params{'jobid'});
}
# Submit a job
else {
# Multiple input sequence mode, assume fasta format.
if (defined($params{'multifasta'}) && $params{'multifasta'}) {
&multi_submit_job();
}
# Entry identifier list file.
elsif ((defined($params{'sequence'}) && $params{'sequence'} =~ m/^\@/)
|| (defined($ARGV[0]) && $ARGV[0] =~ m/^\@/)) {
my $list_filename = $params{'sequence'} || $ARGV[0];
$list_filename =~ s/^\@//;
&list_file_submit_job($list_filename);
}
# Default: single sequence/identifier.
else {
# Warn for invalid batch only option use.
if (defined($params{'useSeqId'}) && $params{'useSeqId'}) {
print STDERR "Warning: --useSeqId option ignored.\n";
delete $params{'useSeqId'};
}
if (defined($params{'maxJobs'}) && $params{'maxJobs'} > 1) {
print STDERR "Warning: --maxJobs option ignored.\n";
$params{'maxJobs'} = 1;
}
# Load the sequence data and submit.
&submit_job(&load_data());
}
}
=head1 FUNCTIONS
=cut
### Wrappers for REST resources ###
=head2 rest_user_agent()
Get a LWP UserAgent to use to perform REST requests.
my $ua = &rest_user_agent();
=cut
sub rest_user_agent() {
print_debug_message('rest_user_agent', 'Begin', 21);
# Create an LWP UserAgent for making HTTP calls.
my $ua = LWP::UserAgent->new();
# Set 'User-Agent' HTTP header to identifiy the client.
my $revisionNumber = 0;
$revisionNumber = "Revision: " . $version;
$ua->agent("EBI-Sample-Client/$revisionNumber ($scriptName; $OSNAME) " . $ua->agent());
# Configure HTTP proxy support from environment.
$ua->env_proxy;
print_debug_message('rest_user_agent', 'End', 21);
return $ua;
}
=head2 rest_error()
Check a REST response for an error condition. An error is mapped to a die.
&rest_error($response, $content_data);
=cut
sub rest_error() {
print_debug_message('rest_error', 'Begin', 21);
my $response = shift;
my $contentdata;
if (scalar(@_) > 0) {
$contentdata = shift;
}
if (!defined($contentdata) || $contentdata eq '') {
$contentdata = $response->content();
}
# Check for HTTP error codes
if ($response->is_error) {
my $error_message = '';
# HTML response.
if ($contentdata =~ m/<h1>([^<]+)<\/h1>/) {
$error_message = $1;
}
# XML response.
elsif ($contentdata =~ m/<description>([^<]+)<\/description>/) {
$error_message = $1;
}
# die 'http status: ' . $response->code . ' ' . $response->message . ' ' . $error_message;
}
print_debug_message('rest_error', 'End', 21);
}
=head2 rest_request()
Perform a REST request (HTTP GET).
my $response_str = &rest_request($url);
=cut
sub rest_request {
print_debug_message('rest_request', 'Begin', 11);
my $requestUrl = shift;
print_debug_message('rest_request', 'URL: ' . $requestUrl, 11);
# Get an LWP UserAgent.
$ua = &rest_user_agent() unless defined($ua);
# Available HTTP compression methods.
my $can_accept;
eval {
$can_accept = HTTP::Message::decodable();
};
$can_accept = '' unless defined($can_accept);
# Perform the request
my $response = $ua->get($requestUrl,
'Accept-Encoding' => $can_accept, # HTTP compression.
);
print_debug_message('rest_request', 'HTTP status: ' . $response->code,
11);
print_debug_message('rest_request',
'response length: ' . length($response->content()), 11);
print_debug_message('rest_request',
'request:' . "\n" . $response->request()->as_string(), 32);
print_debug_message('rest_request',
'response: ' . "\n" . $response->as_string(), 32);
# Unpack possibly compressed response.
my $retVal;
if (defined($can_accept) && $can_accept ne '') {
$retVal = $response->decoded_content();
}
# If unable to decode use orginal content.
$retVal = $response->content() unless defined($retVal);
# Check for an error.
&rest_error($response, $retVal);
print_debug_message('rest_request', 'retVal: ' . $retVal, 12);
print_debug_message('rest_request', 'End', 11);
# Return the response data
return $retVal;
}
=head2 rest_get_parameters()
Get list of tool parameter names.
my (@param_list) = &rest_get_parameters();
=cut
sub rest_get_parameters {
print_debug_message('rest_get_parameters', 'Begin', 1);
my $url = $baseUrl . '/parameters/';
my $param_list_xml_str = rest_request($url);
my $param_list_xml = XMLin($param_list_xml_str);
my (@param_list) = @{$param_list_xml->{'id'}};
print_debug_message('rest_get_parameters', 'End', 1);
return(@param_list);
}
=head2 rest_get_parameter_details()
Get details of a tool parameter.
my $paramDetail = &rest_get_parameter_details($param_name);
=cut
sub rest_get_parameter_details {
print_debug_message('rest_get_parameter_details', 'Begin', 1);
my $parameterId = shift;
print_debug_message('rest_get_parameter_details',
'parameterId: ' . $parameterId, 1);
my $url = $baseUrl . '/parameterdetails/' . $parameterId;
my $param_detail_xml_str = rest_request($url);
my $param_detail_xml = XMLin($param_detail_xml_str);
print_debug_message('rest_get_parameter_details', 'End', 1);
return($param_detail_xml);
}
=head2 rest_run()
Submit a job.
my $job_id = &rest_run($email, $title, \%params );
=cut
sub rest_run {
print_debug_message('rest_run', 'Begin', 1);
my $email = shift;
my $title = shift;
my $params = shift;
$email = '' if (!$email);
print_debug_message('rest_run', 'email: ' . $email, 1);
if (defined($title)) {
print_debug_message('rest_run', 'title: ' . $title, 1);
}
print_debug_message('rest_run', 'params: ' . Dumper($params), 1);
# Get an LWP UserAgent.
$ua = &rest_user_agent() unless defined($ua);
# Clean up parameters
my (%tmp_params) = %{$params};
$tmp_params{'email'} = $email;
$tmp_params{'title'} = $title;
foreach my $param_name (keys(%tmp_params)) {
if (!defined($tmp_params{$param_name})) {
delete $tmp_params{$param_name};
}
}
# Submit the job as a POST
my $url = $baseUrl . '/run';
my $response = $ua->post($url, \%tmp_params);
print_debug_message('rest_run', 'HTTP status: ' . $response->code, 11);
print_debug_message('rest_run',
'request:' . "\n" . $response->request()->as_string(), 11);
print_debug_message('rest_run',
'response: ' . length($response->as_string()) . "\n" . $response->as_string(), 11);
# Check for an error.
&rest_error($response);
# The job id is returned
my $job_id = $response->content();
print_debug_message('rest_run', 'End', 1);
return $job_id;
}
=head2 rest_get_status()
Check the status of a job.
my $status = &rest_get_status($job_id);
=cut
sub rest_get_status {
print_debug_message('rest_get_status', 'Begin', 1);
my $job_id = shift;
print_debug_message('rest_get_status', 'jobid: ' . $job_id, 2);
my $status_str = 'UNKNOWN';
my $url = $baseUrl . '/status/' . $job_id;
$status_str = &rest_request($url);
print_debug_message('rest_get_status', 'status_str: ' . $status_str, 2);
print_debug_message('rest_get_status', 'End', 1);
return $status_str;
}
=head2 rest_get_result_types()
Get list of result types for finished job.
my (@result_types) = &rest_get_result_types($job_id);
=cut
sub rest_get_result_types {
print_debug_message('rest_get_result_types', 'Begin', 1);
my $job_id = shift;
print_debug_message('rest_get_result_types', 'jobid: ' . $job_id, 2);
my (@resultTypes);
my $url = $baseUrl . '/resulttypes/' . $job_id;
my $result_type_list_xml_str = &rest_request($url);
my $result_type_list_xml = XMLin($result_type_list_xml_str);
(@resultTypes) = @{$result_type_list_xml->{'type'}};
print_debug_message('rest_get_result_types',
scalar(@resultTypes) . ' result types', 2);
print_debug_message('rest_get_result_types', 'End', 1);
return(@resultTypes);
}
=head2 rest_get_result()
Get result data of a specified type for a finished job.
my $result = rest_get_result($job_id, $result_type);
=cut
sub rest_get_result {
print_debug_message('rest_get_result', 'Begin', 1);
my $job_id = shift;
my $type = shift;
print_debug_message('rest_get_result', 'jobid: ' . $job_id, 1);
print_debug_message('rest_get_result', 'type: ' . $type, 1);
my $url = $baseUrl . '/result/' . $job_id . '/' . $type;
my $result = &rest_request($url);
print_debug_message('rest_get_result', length($result) . ' characters',
1);
print_debug_message('rest_get_result', 'End', 1);
return $result;
}
### Service actions and utility functions ###
=head2 print_debug_message()
Print debug message at specified debug level.
&print_debug_message($method_name, $message, $level);
=cut
sub print_debug_message {
my $function_name = shift;
my $message = shift;
my $level = shift;
if ($level <= $params{'debugLevel'}) {
print STDERR '[', $function_name, '()] ', $message, "\n";
}
}
=head2 print_tool_params()
Print list of tool parameters.
&print_tool_params();
=cut
sub print_tool_params {
print_debug_message('print_tool_params', 'Begin', 1);
my (@param_list) = &rest_get_parameters();
foreach my $param (sort (@param_list)) {
print $param, "\n";
}
print_debug_message('print_tool_params', 'End', 1);
}
=head2 print_param_details()
Print details of a tool parameter.
&print_param_details($param_name);
=cut
sub print_param_details {
print_debug_message('print_param_details', 'Begin', 1);
my $paramName = shift;
print_debug_message('print_param_details', 'paramName: ' . $paramName, 2);
my $paramDetail = &rest_get_parameter_details($paramName);
print $paramDetail->{'name'}, "\t", $paramDetail->{'type'}, "\n";
print $paramDetail->{'description'}, "\n";
if (defined($paramDetail->{'values'}->{'value'})) {
if (ref($paramDetail->{'values'}->{'value'}) eq 'ARRAY') {
foreach my $value (@{$paramDetail->{'values'}->{'value'}}) {
&print_param_value($value);
}
}
else {
&print_param_value($paramDetail->{'values'}->{'value'});
}
}
print_debug_message('print_param_details', 'End', 1);
}
=head2 print_param_value()
Print details of a tool parameter value.
&print_param_details($param_value);
Used by print_param_details() to handle both singluar and array values.
=cut
sub print_param_value {
my $value = shift;
print $value->{'value'};
if ($value->{'defaultValue'} eq 'true') {
print "\t", 'default';
}
print "\n";
print "\t", $value->{'label'}, "\n";
if (defined($value->{'properties'})) {
foreach
my $key (sort ( keys(%{$value->{'properties'}{'property'}}) )) {
if (ref($value->{'properties'}{'property'}{$key}) eq 'HASH'
&& defined($value->{'properties'}{'property'}{$key}{'value'})
) {
print "\t", $key, "\t",
$value->{'properties'}{'property'}{$key}{'value'}, "\n";
}
else {
print "\t", $value->{'properties'}{'property'}{'key'},
"\t", $value->{'properties'}{'property'}{'value'}, "\n";
last;
}
}
}
}
=head2 print_job_status()
Print status of a job.
&print_job_status($job_id);
=cut
sub print_job_status {
print_debug_message('print_job_status', 'Begin', 1);
my $jobid = shift;
print_debug_message('print_job_status', 'jobid: ' . $jobid, 1);
if ($outputLevel > 0) {
print STDERR 'Getting status for job ', $jobid, "\n";
}
my $result = &rest_get_status($jobid);
print "$result\n";
if ($result eq 'FINISHED' && $outputLevel > 0) {
print STDERR "To get results: perl $scriptName --polljob --jobid " . $jobid
. "\n";
}
print_debug_message('print_job_status', 'End', 1);
}
=head2 print_result_types()
Print available result types for a job.
&print_result_types($job_id);
=cut
sub print_result_types {
print_debug_message('result_types', 'Begin', 1);
my $jobid = shift;
print_debug_message('result_types', 'jobid: ' . $jobid, 1);
if ($outputLevel > 0) {
print STDERR 'Getting result types for job ', $jobid, "\n";
}
my $status = &rest_get_status($jobid);
if ($status eq 'QUEUED' || $status eq 'RUNNING') {
print STDERR 'Error: Job status is ', $status,
'. To get result types the job must be finished.', "\n";
}
else {
my (@resultTypes) = &rest_get_result_types($jobid);
if ($outputLevel > 0) {
print STDOUT 'Available result types:', "\n";
}
foreach my $resultType (@resultTypes) {
print STDOUT $resultType->{'identifier'}, "\n";
if (defined($resultType->{'label'})) {
print STDOUT "\t", $resultType->{'label'}, "\n";
}
if (defined($resultType->{'description'})) {
print STDOUT "\t", $resultType->{'description'}, "\n";
}
if (defined($resultType->{'mediaType'})) {
print STDOUT "\t", $resultType->{'mediaType'}, "\n";
}
if (defined($resultType->{'fileSuffix'})) {
print STDOUT "\t", $resultType->{'fileSuffix'}, "\n";
}
}
if ($status eq 'FINISHED' && $outputLevel > 0) {
print STDERR "\n", 'To get results:', "\n",
" perl $scriptName --polljob --jobid " . $params{'jobid'} . "\n",
" perl $scriptName --polljob --outformat <type> --jobid "
. $params{'jobid'} . "\n";
}
}
print_debug_message('result_types', 'End', 1);
}
=head2 submit_job()
Submit a job to the service.
&submit_job($seq);
=cut
sub submit_job {
print_debug_message('submit_job', 'Begin', 1);
# Set input sequence
$params{'sequence'} = shift;
# Load parameters
&load_params();
# Submit the job
my $jobid = &rest_run($params{'email'}, $params{'title'}, \%params);
# Asynchronous submission.
if (defined($params{'asyncjob'})) {
print STDOUT $jobid, "\n";
if ($outputLevel > 0) {
print STDERR
"To check status: perl $scriptName --status --jobid $jobid\n";
}
}
# Simulate synchronous submission serial mode.
else {
if ($outputLevel > 0) {
print STDERR "JobId: $jobid\n";
} else {
print STDERR "$jobid\n";
}
usleep($checkInterval);
# Get results.
&get_results($jobid);
}
print_debug_message('submit_job', 'End', 1);
return $jobid;
}
=head2 load_data()
Load sequence data from file or option specified on the command-line.
&load_data();
=cut
sub load_data {
print_debug_message('load_data', 'Begin', 1);
my $retSeq;
# Query sequence
if (defined($ARGV[0])) { # Bare option
if (-f $ARGV[0] || $ARGV[0] eq '-') { # File
$retSeq = &read_file($ARGV[0]);
}
else { # DB:ID or sequence
$retSeq = $ARGV[0];
}
}
if ($params{'sequence'}) { # Via --sequence
if (-f $params{'sequence'} || $params{'sequence'} eq '-') { # File
$retSeq = &read_file($params{'sequence'});
}
else { # DB:ID or sequence
$retSeq = $params{'sequence'};
}
}
print_debug_message('load_data', 'End', 1);
return $retSeq;
}
=head2 load_params()
Load job parameters from command-line options.
&load_params();
=cut
sub load_params {
print_debug_message('load_params', 'Begin', 1);
# Pass default values and fix bools (without default value)
print_debug_message('load_params', 'End', 1);
}
=head2 client_poll()
Client-side job polling.
&client_poll($job_id);
=cut
sub client_poll {
print_debug_message('client_poll', 'Begin', 1);
my $jobid = shift;
my $status = 'QUEUED';
# Check status and wait if not finished. Terminate if three attempts get "ERROR".
my $errorCount = 0;
while ($status eq 'RUNNING'
|| $status eq 'QUEUED'
|| ($status eq 'ERROR' && $errorCount < 2)) {
$status = rest_get_status($jobid);
print STDERR "$status\n" if ($outputLevel > 0);
if ($status eq 'ERROR') {
$errorCount++;
}
elsif ($errorCount > 0) {
$errorCount--;
}
if ($status eq 'RUNNING'
|| $status eq 'QUEUED'
|| $status eq 'ERROR') {
# Wait before polling again.
usleep($checkInterval);
}
}
print_debug_message('client_poll', 'End', 1);
return $status;
}
=head2 get_results()
Get the results for a job identifier.
&get_results($job_id);
=cut
sub get_results {
print_debug_message('get_results', 'Begin', 1);
my $jobid = shift;
print_debug_message('get_results', 'jobid: ' . $jobid, 1);
my $output_basename = $jobid;
# Verbose
if ($outputLevel > 1) {
print 'Getting results for job ', $jobid, "\n";
}
# Check status, and wait if not finished
client_poll($jobid);
# Default output file names use JobId, however the name can be specified...
if (defined($params{'outfile'})) {
$output_basename = $params{'outfile'};
}
# Use JobId if output file name is not defined
else {
unless (defined($params{'outfile'})) {
$params{'outfile'} = $jobid;
$output_basename = $jobid;
}
}
# Get list of data types
my (@resultTypes) = rest_get_result_types($jobid);
# Get the data and write it to a file
if (defined($params{'outformat'})) {
# Specified data type
# check to see if there are multiple formats (comma separated)
my $sep = ",";
my (@multResultTypes);
if ($params{'outformat'} =~ /$sep/) {
@multResultTypes = split(',', $params{'outformat'});
}
else {
$multResultTypes[0] = $params{'outformat'};
}
# check if the provided formats are recognised
foreach my $inputType (@multResultTypes) {
my $expectation = 0;
foreach my $resultType (@resultTypes) {
if ($resultType->{'identifier'} eq $inputType && $expectation eq 0) {
$expectation = 1;
}
}
if ($expectation ne 1) {
die 'Error: unknown result format "' . $inputType . '"';
}
}
# if so get the files
my $selResultType;
foreach my $resultType (@resultTypes) {
if (grep {$_ eq $resultType->{'identifier'}} @multResultTypes) {
$selResultType = $resultType;
my $result = rest_get_result($jobid, $selResultType->{'identifier'});
if (defined($params{'outfile'}) && $params{'outfile'} eq '-') {
write_file($params{'outfile'}, $result);
}
else {
write_file(
$output_basename . '.'
. $selResultType->{'identifier'} . '.'
. $selResultType->{'fileSuffix'},
$result
);
}
}
}
}
else { # Data types available
# Write a file for each output type
for my $resultType (@resultTypes) {
if ($outputLevel > 1) {
print STDERR 'Getting ', $resultType->{'identifier'}, "\n";
}
my $result = rest_get_result($jobid, $resultType->{'identifier'});
if (defined($params{'outfile'}) && $params{'outfile'} eq '-') {
write_file($params{'outfile'}, $result);
}
else {
write_file(
$output_basename . '.'
. $resultType->{'identifier'} . '.'
. $resultType->{'fileSuffix'},
$result
);
}
}
}
print_debug_message('get_results', 'End', 1);
}
=head2 read_file()
Read a file into a scalar. The special filename '-' can be used to read from
standard input (STDIN).
my $data = &read_file($filename);
=cut
sub read_file {
print_debug_message('read_file', 'Begin', 1);
my $filename = shift;
print_debug_message('read_file', 'filename: ' . $filename, 2);
my ($content, $buffer);
if ($filename eq '-') {
while (sysread(STDIN, $buffer, 1024)) {
$content .= $buffer;
}
}
else {
# File
open(my $FILE, '<', $filename)
or die "Error: unable to open input file $filename ($!)";
while (sysread($FILE, $buffer, 1024)) {
$content .= $buffer;
}
close($FILE);
}
print_debug_message('read_file', 'End', 1);
return $content;
}
=head2 write_file()
Write data to a file. The special filename '-' can be used to write to
standard output (STDOUT).
&write_file($filename, $data);
=cut
sub write_file {
print_debug_message('write_file', 'Begin', 1);
my ($filename, $data) = @_;
print_debug_message('write_file', 'filename: ' . $filename, 2);
if ($outputLevel > 0) {
print STDERR 'Creating result file: ' . $filename . "\n";
}
if ($filename eq '-') {
print STDOUT $data;
}
else {
open(my $FILE, '>', $filename)
or die "Error: unable to open output file $filename ($!)";
syswrite($FILE, $data);
close($FILE);
}
print_debug_message('write_file', 'End', 1);
}
=head2 usage()
Print program usage message.
&usage();
=cut
sub usage {
print STDERR <<EOF
EMBL-EBI EMBOSS cons Perl Client:
Consensus sequences with EMBOSS Cons.
[Required (for job submission)]
--email E-mail address.
--sequence Sequence similarity search result (e.g. BLAST or FASTA
search report) or a multiple sequence alignment.
--stype Defines the type of the sequences to be aligned.
[Optional]
--plurality Cut-off for the number of positive matches below which there
is no consensus.
--setcase The threshold for the positive matches above which the
consensus is in upper-case and below which the consensus is
in lower-case.
--name Name of the consensus sequence.
--identity The required number of identities at a site for it to give a
consensus at that position.
--matrix Default substitution scoring matrices.
[General]
-h, --help Show this help message and exit.
--asyncjob Forces to make an asynchronous query.
--title Title for job.
--status Get job status.
--resultTypes Get available result types for job.
--polljob Poll for the status of a job.
--pollFreq Poll frequency in seconds (default 3s).
--jobid JobId that was returned when an asynchronous job was submitted.
--outfile File name for results (default is JobId; for STDOUT).
--outformat Result format(s) to retrieve. It accepts comma-separated values.