clustalw-client.pl

#!/usr/bin/perl
  
# usage: perl wabi-client conf.json
  
use strict;
use warnings;
use LWP::UserAgent;
use HTTP::Request::Common;
use JSON qw/encode_json decode_json/;
  
# JSONファイルからweb APIにPOSTする値を取り出す。
my $json_file = $ARGV[0];
  
open IN, $json_file or die;
my $json_in = '';
while (<in>) {
        chomp;
        $json_in .= $_;
}
close IN;
my $data_ref = decode_json($json_in);
my %data = %$data_ref;
  
my $format            = 'text';
my $url               = $data{'urlStr'};
my $infile            = $data{'infile'};
my $profile1_file     = $data{'profile1'};
my $profile2_file     = $data{'profile2'};
my $guidetree1_file   = $data{'guidetree1'};
my $guidetree2_file   = $data{'guidetree2'};
my $pwdnamatrix_file  = $data{'pwdnamatrix'};
my $pwaamatrix_file   = $data{'pwaamatrix'};
my $dnamatrix_file    = $data{'dnamatrix'};
my $aamatrix_file     = $data{'aamatrix'};
my $parameters        = $data{'parameters'};
my $result            = $data{'result'};
my $address           = $data{'address'};
  
# Multiple Alignmentを行う。
print "Execute multiple sequence alignment.\n";
  
my $input_data        = '';
my $profile1_data     = '';
my $profile2_data     = '';
my $guidetree1_data   = '';
my $guidetree2_data   = '';
my $pwdnamatrix_data  = '';
my $pwaamatrix_data   = '';
my $dnamatrix_data    = '';
my $aamatrix_data     = '';
  
$input_data        = &open_read($infile) if $infile;
$profile1_data     = &open_read($profile1_file) if $profile1_file;
$profile2_data     = &open_read($profile2_file) if $profile2_file;
$guidetree1_data   = &open_read($guidetree1_file) if $guidetree1_file;
$guidetree2_data   = &open_read($guidetree2_file) if $guidetree2_file;
$pwdnamatrix_data  = &open_read($pwdnamatrix_file) if $pwdnamatrix_file;
$pwaamatrix_data   = &open_read($pwaamatrix_file) if $pwaamatrix_file;
$dnamatrix_data    = &open_read($dnamatrix_file) if $dnamatrix_file;
$aamatrix_data     = &open_read($aamatrix_file) if $aamatrix_file;
  
# 取り出した値をPOSTする。
my %post_data = (
        'querySequence' => $input_data,
        'profile1'      => $profile1_data,
        'profile2'      => $profile2_data,
        'guidetree1'    => $guidetree1_data,
        'guidetree2'    => $guidetree2_data,
        'pwDnaMatrix'   => $pwdnamatrix_data,
        'pwAaMatrix'    => $pwaamatrix_data,
        'dnaMatrix'     => $dnamatrix_data,
        'aaMatrix'      => $aamatrix_data,
        'format'        => $format,
        'parameters'    => $parameters,
        'result'        => $result,
        'address'       => $address,
);
  
my $request = POST($url, \%post_data);
  
my $ua = LWP::UserAgent -> new;
my $res = $ua -> request( $request );
  
my $request_id = '';
if ($res->is_success) {
        my $content = $res->content;
        if ($content =~ /requestId: (.*)/) {
                $request_id = $1;
        }
} else {
        my $content = $res->content;
        print "$content\n";
        die $res->status_line;
}
print "request-ID: $request_id\n";
  
# request-IDでGETする。
my $status = '';
while (1) {
        $request = GET($url . $request_id);
        $res = $ua -> request( $request );
        if ($res->is_success) {
                my $content = $res->content;
                if ($content =~/status: (.*)/) {
                        $status = $1;
                }
        } else {
                die $res->status_line;
        }
        print "$status\n";
        if ($status eq 'waiting') {
                sleep(10);
        } elsif ($status eq 'running') {
                sleep(10);
        } elsif ($status eq 'finished') {
                last;
        }
}
  
# clustalwの出力結果を取得する。
$request = GET($url . $request_id . '?info=result');
$res = $ua -> request( $request );
if ($res->is_success) {
        open OUT, ">${request_id}.txt" or die;
        print OUT $res->content;
        close OUT;
        print "ClustalW2 result is outputed to ${request_id}.txt\n";
} else {
        die $res->status_line;
}
  
$request = GET($url . $request_id . '?info=result_guide1');
$res = $ua -> request( $request );
if ($res->is_success) {
        open OUT, ">${request_id}_guidetree1.txt" or die;
        print OUT $res->content;
        close OUT;
        print "Guide Tree 1 is outputed to ${request_id}_guidetree1.txt\n";
} else {
        if ($res->code != 404) {
                die $res->status_line;
        }
}
  
$request = GET($url . $request_id . '?info=result_guide2');
$res = $ua -> request( $request );
if ($res->is_success) {
        open OUT, ">${request_id}_guidetree2.txt" or die;
        print OUT $res->content;
        close OUT;
        print "Guide Tree 2 is outputed to ${request_id}_guidetree1.txt\n";
} else {
        if ($res->code != 404) {
                die $res->status_line;
        }
}
  
$request = GET($url . $request_id . '?info=result_pim');
$res = $ua -> request( $request );
if ($res->is_success) {
        open OUT, ">${request_id}_pim.txt" or die;
        print OUT $res->content;
        close OUT;
        print "PIM file is outputed to ${request_id}_pim.txt\n";
} else {
        if ($res->code != 404) {
                die $res->status_line;
        }
}
  
sub open_read {
        my $file = $_[0];
        my $content = '';
        open FILE, $file or die;
        while (<file>) {
                $content .= $_;
        }
        close FILE;
        return $content;
}
</file></in>