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fasta.pl
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#!/usr/bin/env perl
=head1 NAME
fasta.pl
=head1 DESCRIPTION
FASTA (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/fasta';
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
);
my @database;
# Default parameter values (should get these from the service)
GetOptions(
# Tool specific options
'program=s' => \$params{'program'}, # The FASTA program to be used for the Sequence Similarity Search
'stype=s' => \$params{'stype'}, # Indicates if the query sequence is protein, DNA or RNA. Used to force FASTA to interpret the input sequence as specified type of sequence (via. the '-p', '-n' or '-U' options), this prevents issues when using nucleotide sequences that contain many ambiguous residues.
'matrix=s' => \$params{'matrix'}, # (Protein searches) The substitution matrix used for scoring alignments when searching the database. Target identity is the average alignment identity the matrix would produce in the absence of homology and can be used to compare different matrix types. Alignment boundaries are more accurate when the alignment identity matches the target identity percentage.
'match_scores=s' => \$params{'match_scores'}, # (Nucleotide searches) The match score is the bonus to the alignment score when matching the same base. The mismatch is the penalty when failing to match.
'gapopen=i' => \$params{'gapopen'}, # Score for the first residue in a gap.
'gapext=i' => \$params{'gapext'}, # Score for each additional residue in a gap.
'hsps' => \$params{'hsps'}, # Turn on/off the display of all significant alignments between query and library sequence.
'expupperlim=f' => \$params{'expupperlim'}, # Limits the number of scores and alignments reported based on the expectation value. This is the maximum number of times the match is expected to occur by chance.
'explowlim=f' => \$params{'explowlim'}, # Limit the number of scores and alignments reported based on the expectation value. This is the minimum number of times the match is expected to occur by chance. This allows closely related matches to be excluded from the result in favor of more distant relationships.
'strand=s' => \$params{'strand'}, # For nucleotide sequences specify the sequence strand to be used for the search. By default both upper (provided) and lower (reverse complement of provided) strands are used, for single stranded sequences searching with only the upper or lower strand may provide better results.
'hist' => \$params{'hist'}, # Turn on/off the histogram in the FASTA result. The histogram gives a qualitative view of how well the statistical theory fits the similarity scores calculated by the program.
'scores=i' => \$params{'scores'}, # Maximum number of match score summaries reported in the result output.
'alignments=i' => \$params{'alignments'}, # Maximum number of match alignments reported in the result output.
'scoreformat=s' => \$params{'scoreformat'}, # Different score report formats.
'stats=s' => \$params{'stats'}, # The statistical routines assume that the library contains a large sample of unrelated sequences. Options to select what method to use include regression, maximum likelihood estimates, shuffles, or combinations of these.
'annotfeats' => \$params{'annotfeats'}, # Turn on/off annotation features. Annotation features shows features from UniProtKB, such as variants, active sites, phospho-sites and binding sites that have been found in the aligned region of the database hit. To see the annotation features in the results after this has been enabled, select sequences of interest and click to 'Show' Alignments. This option also enables a new result tab (Domain Diagrams) that highlights domain regions.
'annotsym=s' => \$params{'annotsym'}, # Specify the annotation symbols.
'dbrange=s' => \$params{'dbrange'}, # Specify the sizes of the sequences in a database to search against. For example: 100-250 will search all sequences in a database with length between 100 and 250 residues, inclusive.
'seqrange=s' => \$params{'seqrange'}, # Specify a range or section of the input sequence to use in the search. Example: Specifying '34-89' in an input sequence of total length 100, will tell FASTA to only use residues 34 to 89, inclusive.
'filter=s' => \$params{'filter'}, # Filter regions of low sequence complexity. This can avoid issues with low complexity sequences where matches are found due to composition rather then meaningful sequence similarity. However in some cases filtering also masks regions of interest and so should be used with caution.
'transltable=i' => \$params{'transltable'}, # Query Genetic code to use in translation
'sequence=s' => \$params{'sequence'}, # The query 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.
'database=s' => \@database, # The databases to run the sequence similarity search against. Multiple databases can be used at the same time
'ktup=i' => \$params{'ktup'}, # FASTA uses a rapid word-based lookup strategy to speed the initial phase of the similarity search. The KTUP is used to control the sensitivity of the search. Lower values lead to more sensitive, but slower searches.
# 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
'multifasta' => \$params{'multifasta'}, # Multiple fasta input
'useSeqId' => \$params{'useSeqId'}, # Seq Id file name
'maxJobs=i' => \$params{'maxJobs'}, # Max. parallel jobs
'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'}}
$params{"database"} = [@database];
# 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;
my $seq_id = 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, $seq_id);
}
print_debug_message('submit_job', 'End', 1);
return $jobid;
}
=head2 multi_submit_job()
Submit multiple jobs assuming input is a collection of fasta formatted sequences.
&multi_submit_job();
=cut
sub multi_submit_job {
print_debug_message('multi_submit_job', 'Begin', 1);
my (@filename_list) = ();
# Query sequence
if (defined($ARGV[0])) { # Bare option
if (-f $ARGV[0] || $ARGV[0] eq '-') { # File
push(@filename_list, $ARGV[0]);
}
else {
warn 'Warning: Input file "' . $ARGV[0] . '" does not exist';
}
}
if ($params{'sequence'}) { # Via --sequence
if (-f $params{'sequence'} || $params{'sequence'} eq '-') { # File
push(@filename_list, $params{'sequence'});
}
else {
warn 'Warning: Input file "'
. $params{'sequence'}
. '" does not exist';
}
}
# Job identifier tracking for parallel execution.
my @jobid_list = ();
my $job_number = 0;
$/ = '>';
foreach my $filename (@filename_list) {
my $INFILE;
if ($filename eq '-') { # STDIN.
open($INFILE, '<-')
or die 'Error: unable to STDIN (' . $! . ')';
}
else { # File.
open($INFILE, '<', $filename)
or die 'Error: unable to open file '
. $filename . ' ('
. $! . ')';
}
while (<$INFILE>) {
my $seq = $_;
$seq =~ s/>$//;
if ($seq =~ m/(\S+)/) {
my $seq_id = $1;
print STDERR "Submitting job for: $seq_id\n"
if ($outputLevel > 0);
$seq = '>' . $seq;
&print_debug_message('multi_submit_job', $seq, 11);
$job_number++;
my $job_id = &submit_job($seq, $seq_id);
my $job_info_str = sprintf('%s %d %d', $job_id, 0, $job_number);
push(@jobid_list, $job_info_str);
}
# Parallel mode, wait for job(s) to finish to free slots.
while ($params{'maxJobs'} > 1
&& scalar(@jobid_list) >= $params{'maxJobs'}) {
&_job_list_poll(\@jobid_list);
print_debug_message('multi_submit_job',
'Remaining jobs: ' . scalar(@jobid_list), 1);
}
}
close $INFILE;
}
# Parallel mode, wait for remaining jobs to finish.
while ($params{'maxJobs'} > 1 && scalar(@jobid_list) > 0) {
&_job_list_poll(\@jobid_list);
print_debug_message('multi_submit_job',
'Remaining jobs: ' . scalar(@jobid_list), 1);
}
print_debug_message('multi_submit_job', 'End', 1);
}
=head2 _job_list_poll()
Poll the status of a list of jobs and fetch results for finished jobs.
while(scalar(@jobid_list) > 0) {
&_job_list_poll(\@jobid_list);
}
=cut
sub _job_list_poll {
print_debug_message('_job_list_poll', 'Begin', 1);
my $jobid_list = shift;
print_debug_message('_job_list_poll', 'Num jobs: ' . scalar(@$jobid_list),
11);
# Loop though job Id list polling job status.
for (my $jobNum = (scalar(@$jobid_list) - 1); $jobNum > -1; $jobNum--) {
my ($jobid, $seq_id, $error_count, $job_number) =
split(/\s+/, $jobid_list->[$jobNum]);
print_debug_message('_job_list_poll', 'jobNum: ' . $jobNum, 12);
print_debug_message('_job_list_poll',
'Job info: ' . $jobid_list->[$jobNum], 12);
# Get job status.
my $job_status = &rest_get_status($jobid);
print_debug_message('_job_list_poll', 'Status: ' . $job_status, 12);
# Fetch results and remove finished/failed jobs from list.
if (
!(
$job_status eq 'RUNNING'
|| $job_status eq 'QUEUED'
|| ($job_status eq 'ERROR'
&& $error_count < $maxErrorStatusCount)
)
) {
if ($job_status eq 'ERROR' || $job_status eq 'FAILED') {
print STDERR
"Warning: job $jobid failed for sequence $job_number: $seq_id\n";
}
# Duplicated getting results.
#&get_results($jobid, $seq_id);
splice(@$jobid_list, $jobNum, 1);
}
else {
# Update error count, increment for new error or clear old errors.
if ($job_status eq 'ERROR') {
$error_count++;
}
elsif ($error_count > 0) {
$error_count--;
}
# Update job tracking info.
my $job_info_str = sprintf('%s %s %d %d',
$jobid, $seq_id, $error_count, $job_number);
$jobid_list->[$jobNum] = $job_info_str;
}
}
print_debug_message('_job_list_poll', 'Num jobs: ' . scalar(@$jobid_list),
11);
print_debug_message('_job_list_poll', 'End', 1);
}
=head2 list_file_submit_job()
Submit multiple jobs using a file containing a list of entry identifiers as
input.
&list_file_submit_job($list_filename)
=cut
sub list_file_submit_job {
print_debug_message('list_file_submit_job', 'Begin', 1);
my $filename = shift;
# Open the file of identifiers.
my $LISTFILE;
if ($filename eq '-') { # STDIN.
open($LISTFILE, '<-')
or die 'Error: unable to STDIN (' . $! . ')';
}
else { # File.
open($LISTFILE, '<', $filename)
or die 'Error: unable to open file ' . $filename . ' (' . $! . ')';
}
# Job identifier tracking for parallel execution.
my @jobid_list = ();
my $job_number = 0;
# Iterate over identifiers, submitting each job
while (<$LISTFILE>) {
my $line = $_;
chomp($line);
if ($line ne '') {
&print_debug_message('list_file_submit_job', 'line: ' . $line, 2);
if ($line =~ m/\w:\w/) {
# Check this is an identifier
my $seq_id = $line;
print STDERR "Submitting job for: $seq_id\n"
if ($outputLevel > 0);
$job_number++;
my $job_id = &submit_job($seq_id, $seq_id);
my $job_info_str =
sprintf('%s %s %d %d', $job_id, $seq_id, 0, $job_number);
push(@jobid_list, $job_info_str);
}
else {
print STDERR
"Warning: line \"$line\" is not recognised as an identifier\n";
}
# Parallel mode, wait for job(s) to finish to free slots.
while ($params{'maxJobs'} > 1
&& scalar(@jobid_list) >= $params{'maxJobs'}) {
&_job_list_poll(\@jobid_list);
print_debug_message('list_file_submit_job',
'Remaining jobs: ' . scalar(@jobid_list), 1);
}
}
}
close $LISTFILE;
# Parallel mode, wait for remaining jobs to finish.
while ($params{'maxJobs'} > 1 && scalar(@jobid_list) > 0) {
&_job_list_poll(\@jobid_list);
print_debug_message('list_file_submit_job',
'Remaining jobs: ' . scalar(@jobid_list), 1);
}
print_debug_message('list_file_submit_job', 'End', 1);
}
=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 $retSeq;
}
=head2 load_params()
Load job parameters from command-line options.
&load_params();
=cut
sub load_params {
print_debug_message('load_params', 'Begin', 1);
# Pass default values and fix bools (without default value)
if (!$params{'hsps'}) {
$params{'hsps'} = 'false'
}
if (!$params{'explowlim'}) {
$params{'explowlim'} = '0'
}