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genewise.pl
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#!/usr/bin/env perl
=head1 NAME
genewise.pl
=head1 DESCRIPTION
Genewise (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/genewise';
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
'para' => \$params{'para'}, # Show parameters in the output alignmment, as in genewise.
'pretty' => \$params{'pretty'}, # Show pretty ASCII alignment viewing, as in genewise.
'genes' => \$params{'genes'}, # Show gene structure, as in genewise
'trans' => \$params{'trans'}, # Show protein translation, breaking at frameshifts.
'cdna' => \$params{'cdna'}, # Show cDNA, as in genewise.
'embl' => \$params{'embl'}, # EMBL feature table format with CDS key.
'ace' => \$params{'ace'}, # Show Ace file gene structure, as in genewise.
'gff' => \$params{'gff'}, # Show Gene Feature Format file, as in genewise.
'diana' => \$params{'diana'}, # Show EMBL FT format suitable for diana.
'init=s' => \$params{'init'}, # Model in local/global mode. You should only put the model in global mode if you expect your protein homolog to have homology from start to end to the gene in the DNA sequence.
'splice=s' => \$params{'splice'}, # Using splice model or GT/AG? Use the full blown model for splice sites, or a simplistic GT/AG. Generally if you are using a DNA sequence which is from human or worm, then leave this on. If you are using a very different (eg plant) species, switch it off.
'random=s' => \$params{'random'}, # The probability of the model has to compared to an alternative model (in fact to all alternative models which are possible) to allow proper Bayesian inference. This causes considerable difficulty in these algorithms because from a algorithmical point of view we would probably like to use an alternative model which is a single state, like the random model in profile-HMMs, where we can simply 'log-odd' the scored model, whereas from a biological point of view we probably want to use a full gene predicting alternative model. In addition we need to account for the fact that the protein HMM or protein homolog probably does not extend over all the gene sequence, nor in fact does the gene have to be the only gene in the DNA sequence. This means that there are very good splice sites/poly-pyrimidine tracts outside of the 'matched' alignment can severely de-rail the alignment.
'alg=s' => \$params{'alg'}, # The solutions is different in the genewise21:93 compared to the genewise 6:23 algorithms. (1) In 6:23 we force the external match portions of the homology model to be identical to the alternative model, thus cancelling each other out. This is a pretty gross approximation and is sort of equivalent to the intron tie'ing. It makes things algorithmically easier... However this means a) 6:23 is nowhere near a probabilistic model and b) you really have to used a tied intron model in 6:23 otherwise very bad edge effects (final introns being ridiculously long) occur. (2) In 21:93 we have a full probabilistic model on each side of the homology segment. This is not reported in the -pretty output but you can see it in the -alb output if you like. Do not trust the gene model outside of the homology segment however. By having these external gene model parts we can use all the gene model features safe in the knowledge that if the homology segments do not justify the match then the external part of the model will soak up the additional intron/py-tract/splice site biases.
'asequence=s' => \$params{'asequence'}, # The protein sequence can be entered directly into this form. The sequence can be in GCG, FASTA, EMBL (Nucleotide only), GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot (Protein only) format. A partially formatted sequence is not accepted. Adding a return to the end of the sequence may help certain applications understand the input. Note that directly using data from word processors may yield unpredictable results as hidden/control characters may be present. There is a limit of 1MB for the sequence entry.
'bsequence=s' => \$params{'bsequence'}, # The DNA sequence to be compared can be entered directly into the form. The sequence must be in a recognised format eg. GCG, FASTA, EMBL, GenBank. Partially formatted sequences are not accepted. Adding a return to the end of the sequence may help certain applications understand the input. Note that directly using data from word processors may yield unpredictable results as hidden/control characters may be present. There is a limit of 1MB for the sequence entry.
# 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'}
|| $params{'paramDetail'}
)
&& !((defined($ARGV[0]) && defined($ARGV[1])) ||
(defined($params{'asequence'}) && defined($params{'bsequence'})))
) {
# Bad argument combination, so print error message and usage
print STDERR 'Error: bad option combination', "\n";
&usage();
exit(1);
}
# Get parameters list
elsif ($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{'asequence'} = shift;
$params{'bsequence'} = 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 $jobid;
}
=head2 load_data()
Load sequence data from file or option specified on the command-line.
&load_data();
=cut
sub load_data {
print_debug_message('load_data', 'Begin', 1);
my @retSeq = ();
# First sequence
if (defined($ARGV[0])) { # Bare option
if (-f $ARGV[0] || $ARGV[0] eq '-') { # File
$retSeq[0] = &read_file($ARGV[0]);
}
else { # DB:ID or raw sequence
$retSeq[0] = $ARGV[0];
}
}
if ($params{'asequence'}) { # Via --sequence
if (-f $params{'asequence'} || $params{'asequence'} eq '-') { # File
$retSeq[0] = &read_file($params{'asequence'});
}
else { # DB:ID or sequence
$retSeq[0] = $params{'asequence'};
}
}
# Second sequence
if (defined($ARGV[1])) { # Bare option
if (-f $ARGV[1] || $ARGV[1] eq '-') { # File
$retSeq[1] = &read_file($ARGV[1]);
}
else { # DB:ID or raw sequence
$retSeq[1] = $ARGV[1];
}
}
if ($params{'bsequence'}) { # Via --sequence
if (-f $params{'bsequence'} || $params{'bsequence'} eq '-') { # File
$retSeq[1] = &read_file($params{'bsequence'});
}
else { # DB:ID or sequence
$retSeq[1] = $params{'bsequence'};
}
}
print_debug_message('load_data', 'End', 1);
return @retSeq;
}
=head2 load_params()
Load job parameters from command-line options.
&load_params();
=cut
sub load_params {
print_debug_message('load_params', 'Begin', 1);
# Pass default values and fix bools (without default value)
if (!$params{'para'}) {
$params{'para'} = 'true'
}
if (!$params{'pretty'}) {
$params{'pretty'} = 'true'
}
if (!$params{'genes'}) {
$params{'genes'} = 'true'
}
if (!$params{'trans'}) {
$params{'trans'} = 'true'
}
if (!$params{'cdna'}) {
$params{'cdna'} = 'true'
}
if (!$params{'embl'}) {
$params{'embl'} = 'true'
}
if (!$params{'ace'}) {
$params{'ace'} = 'true'
}
if (!$params{'gff'}) {
$params{'gff'} = 'true'
}
if (!$params{'diana'}) {
$params{'diana'} = 'true'
}
if (!$params{'init'}) {
$params{'init'} = 'local'
}
if (!$params{'splice'}) {
$params{'splice'} = 'flat'
}
if (!$params{'random'}) {
$params{'random'} = 'syn'
}
if (!$params{'alg'}) {
$params{'alg'} = '623'
}
print_debug_message('load_params', 'End', 1);
}
=head2 client_poll()
Client-side job polling.
&client_poll($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)