Mercurial > repos > earlhaminst > smart_domains

annotate smart-domain.pl @ 1:8c24cc7431aa draft default tip

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"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 411fa9c106996050b2d2e8027e14d2068f6b14c3"
author earlhaminst
date Tue, 22 Dec 2020 04:29:12 +0000
parents a3b26189fee3
children
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a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
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1 #!/usr/bin/env perl
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
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2 use strict;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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3 use HTTP::Request::Common;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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4 use LWP::UserAgent;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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5 use Pod::Usage;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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6 use Getopt::Long;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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7 use Bio::SeqIO;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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8 use JSON;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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10 my $json = JSON->new->allow_nonref;
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11 #run this script with --help to see the options
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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13 =pod
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a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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15 =head1 NAME
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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17 SMART_batch - submit sequences from a FASTA file to SMART
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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19 =head1 SYNOPSIS
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21 B<SMART_batch.pl> I<options>
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
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23 =head1 DESCRIPTION
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25 Use B<SMART_batch.pl> to submit multiple protein sequences from a FASTA file into the SMART analysis queue. Results are saved into plain text files.
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27 =head1 GENERAL OPTIONS
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30 =over 4
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32 =item B<--help>
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34 display this message
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36 =item B<--inputFile>
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38 FASTA file with sequences to submit
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40 =item B<--outputDirectory>
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42 Directory which will be used to store the results. Will be created if it doesn't exist. Defaults to 'SMART_results'.
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44 =item B<--outputFormat>
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46 Choose prefered output format from txt, json or tabular.
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47 Default is txt.
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49 =back
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51 =head1 ANALYSIS OPTIONS
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53 =over 4
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55 =item B<--includePfam>
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57 Include Pfam domains in the search. (http://pfam.sanger.ac.uk/)
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59 =item B<--includeSignalP>
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61 Include signal peptide predictions. (http://www.cbs.dtu.dk/services/SignalP/)
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63 =item B<--includeRepeats>
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65 Include internal repeat predictions. (http://www.well.ox.ac.uk/rmott/ARIADNE/)
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66
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67 =item B<--includeDISEMBL>
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68
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69 Include predictions of internal protein disorder. (http://dis.embl.de/)
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71 =item B<--includeSchnipsel>
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73 Include predictions of outlier homologues and homologues of known structures. (http://smart.embl.de/help/smart_glossary.shtml#outlier)
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75 =back
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78 =head1 SEE ALSO
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80 SMART Home page : http://smart.embl.de
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81 SMART FAQ : http://smart.embl.de/help/FAQ.shtml
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82
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83 =head1 AUTHORS
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84
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85 Written by Ivica Letunic <ivica@letunic.com>
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87 Modified by Anil Thanki <Anil.Thanki@earlham.ac.uk> to parse output in JSON and tabular format to adapt in Galaxy
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88
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diff changeset
89 =cut
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earlhaminst
parents:
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90
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91 my $submit_url = "http://smart.embl.de/smart/show_motifs.pl";
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
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92 my $job_status_url = "http://smart.embl.de/smart/job_status.pl";
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earlhaminst
parents:
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93 my $output_format = "txt";
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earlhaminst
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diff changeset
94 my ($show_help, $input_file, $output_directory, $do_pfam, $do_signalp, $do_rep, $do_disembl, $do_schnipsel);
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earlhaminst
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95 my $op_r = GetOptions (
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earlhaminst
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96 "help" => \$show_help,
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earlhaminst
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97 "inputFile=s" => \$input_file,
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earlhaminst
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98 "outputDirectory=s" => \$output_directory,
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earlhaminst
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99 "includePfam" => \$do_pfam,
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earlhaminst
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100 "includeSignalP" => \$do_signalp,
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earlhaminst
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101 "includeRepeats" => \$do_rep,
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earlhaminst
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102 "includeDISEMBL" => \$do_disembl,
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earlhaminst
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103 "includeSchnipsel" => \$do_schnipsel,
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earlhaminst
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104 "outputFormat=s" => \$output_format,
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earlhaminst
parents:
diff changeset
105 );
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
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106
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earlhaminst
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107 unless ($input_file) { $show_help = 1; }
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108
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earlhaminst
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109 pod2usage(VERBOSE => 2) if ( $show_help );
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
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110
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earlhaminst
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111 my $ua = LWP::UserAgent->new();
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earlhaminst
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112 my $result = "";
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earlhaminst
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113 $ua->agent("SMARTbatch1.0");
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earlhaminst
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114
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115
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116 print "\nSMART batch analysis\n======================\n";
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earlhaminst
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117
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earlhaminst
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118 unless (defined $output_directory) { $output_directory = 'SMART_results'; }
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earlhaminst
parents:
diff changeset
119 unless (-d $output_directory) { mkdir $output_directory; }
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earlhaminst
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120 unless (-e $input_file) { print STDERR "Input file does not exist."; exit;}
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earlhaminst
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121
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earlhaminst
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122 my $io = new Bio::SeqIO(-format=> 'fasta', -file=> $input_file);
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earlhaminst
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123
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earlhaminst
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124 #process sequences one by one. ALWAYS wait for the results before submitting the next sequence.
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125
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earlhaminst
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126 while (my $seq = $io->next_seq) {
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127 my $seq_id = $seq->display_id;
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earlhaminst
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128 my $output_file;
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earlhaminst
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129 if ($output_format eq "txt")
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130 {
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131 $output_file = $output_directory . "/" . $seq_id . "_SMART_results.txt";
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earlhaminst
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132 } elsif ($output_format eq "tabular")
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133 {
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earlhaminst
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134 $output_file = $output_directory . "/" . $seq_id . "_SMART_results.tabular";
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earlhaminst
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diff changeset
135 } elsif ($output_format eq "json"){
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earlhaminst
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136 $output_file = $output_directory . "/" . $seq_id . "_SMART_results.json";
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earlhaminst
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137 }
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earlhaminst
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diff changeset
138 if (-e $output_file) {
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earlhaminst
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139 my @s = stat($output_file);
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earlhaminst
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140 if ($s[7] == 0) {
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earlhaminst
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141 print "Removing empty results file $output_file.\n";
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earlhaminst
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142 unlink $output_file;
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earlhaminst
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143 } else {
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144 print "Skipping sequence $seq_id because the results file already exists.\n";
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earlhaminst
parents:
diff changeset
145 next;
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146 }
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147 }
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148 print "Submitting sequence $seq_id...\n";
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earlhaminst
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149 #prepare the basic POST data
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diff changeset
150 my %post_content;
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151 $post_content{'SEQUENCE'} = $seq->seq;
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152 $post_content{'TEXTONLY'} = 1;
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153 if ($do_pfam) { $post_content{'DO_PFAM'} = 'DO_PFAM'; }
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earlhaminst
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diff changeset
154 if ($do_signalp) { $post_content{'INCLUDE_SIGNALP'} = 'INCLUDE_SIGNALP'; }
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earlhaminst
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diff changeset
155 if ($do_rep) { $post_content{'DO_PROSPERO'} = 'DO_PROSPERO'; }
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
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diff changeset
156 if ($do_disembl) { $post_content{'DO_DISEMBL'} = 'DO_DISEMBL'; }
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
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157 if ($do_schnipsel) { $post_content{'INCLUDE_BLAST'} = 'INCLUDE_BLAST'; }
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
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158 my $req = POST $submit_url, Content_Type => 'form-data', Content => [ %post_content ];
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earlhaminst
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159 my $response = $ua->request($req);
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earlhaminst
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diff changeset
160 if ($response->is_success()) {
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earlhaminst
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diff changeset
161 my @res = split(/\n/, $response->content);
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
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diff changeset
162 #check if we got the results directly (precomputed results)
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earlhaminst
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163 shift @res if ($res[1] =~ /^--\ SMART\ RESULT/);
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
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diff changeset
164 if ($res[0] =~ /^--\ SMART\ RESULT/) {
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earlhaminst
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165 response_parser($output_file, $response, $output_format);
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
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diff changeset
166 } else {
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167 #we're in the queue, or there was an error
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earlhaminst
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diff changeset
168 my $job_id;
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earlhaminst
parents:
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169 for (my $i = 0; $i <= $#res; $i++) {
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earlhaminst
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170 if ($res[$i] =~ /job_status\.pl\?jobid=(\d+.+?)'/) {
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171 $job_id = $1;
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earlhaminst
parents:
diff changeset
172 last;
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173 }
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diff changeset
174 }
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
175 unless (length $job_id) {
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
176 #there is no job ID, so an error occured
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
177 my $error_file = "$output_directory/$seq_id\_SMART_error.html";
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
178 open (ERR, ">$error_file") or die "Cannot write to $error_file";
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
179 print ERR $response->content;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
180 close ERR;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
181 print "SMART returned an error page, which was saved into '$error_file'.\nPlease check the file for details. Aborting further submissions.\n";
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
182 exit;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
183 } else {
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
184 #we have a jobID, check every 10 seconds until we get the results
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
185 print "Job entered the queue with ID $job_id. Waiting for results.\n";
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
186 my $job_status_req = GET "$job_status_url?jobid=$job_id";
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
187 sleep 5;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
188 while (1) {
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
189 my $job_status_response = $ua->request($job_status_req);
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
190 if ($job_status_response->is_success) {
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
191 #check if we got the results
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
192 my @job_status_res = split(/\n/, $job_status_response->content);
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
193 shift @job_status_res if ($job_status_res[1] =~ /^--\ SMART\ RESULT/);
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
194 if ($job_status_res[0] =~ /^--\ SMART\ RESULT/) {
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
195 response_parser($output_file, $job_status_response, $output_format);
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
196 last;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
197 } else {
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
198 #still in queue
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earlhaminst
parents:
diff changeset
199 sleep 10;
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earlhaminst
parents:
diff changeset
200 }
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
201 } else {
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
202 print "SMART returned a web server error. Full message follows:\n\n";
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
203 print $response->as_string;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
204 die;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
205 }
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
206 }
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
207 }
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
208 }
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
209
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
210 } else {
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
211 print "SMART returned a web server error. Full message follows:\n\n";
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
212 print $response->as_string;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
213 die;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
214 }
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
215 #be nice to other users
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
216 sleep 5;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
217 }
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
218
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
219 sub toJSON{
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
220 my ($text) = @_;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
221
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
222 my @result = split("\n", $text);
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
223 my $line;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
224 my %hash;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
225 my @hashes;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
226 my $json;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
227
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
228 foreach $line (@result)
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
229 {
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
230 if(index($line, "=") > 0){
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
231 my $key = (split(/=/, $line))[0];
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
232 my $value = (split(/=/, $line))[1];
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
233 $hash{$key} = $value;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
234 } elsif(length($line) == 0){
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
235 if (exists $hash{"DOMAIN"})
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
236 {
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
237 $json = encode_json \%hash;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
238 push @hashes, $json;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
239 }
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
240 %hash = ();
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
241 }
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
242 }
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
243
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
244 return @hashes;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
245 }
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
246
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
247 sub response_parser{
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
248 my $output_file = $_[0];
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
249 my $job_status_response = $_[1];
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
250 my $output_format = $_[2];
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
251
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
252
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
253 open (OUT, ">$output_file") or die "Cannot write to $output_file";
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
254 $result = $job_status_response->content;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
255 if ($output_format eq "txt")
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
256 {
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
257 print OUT $result;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
258 } elsif ($output_format eq "tabular")
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
259 {
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
260 my @result = toJSON($result);
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
261
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
262 my $first_row = decode_json $result[0];
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
263 my @keys;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
264 my $counter;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
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265
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
266 foreach my $key(sort keys %$first_row) {
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
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267 print OUT "$key";
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
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268 print OUT "\t" if ++$counter < scalar keys %$first_row;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
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269 push @keys, $key;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
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270 }
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
271 print OUT "\n";
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
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272
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
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273 my $counter;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
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274
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
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275 foreach my $line (@result)
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
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276 {
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
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277 my $first_row = decode_json $line;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
278 my $counter;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
279 foreach my $key (@keys)
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
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280 {
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
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281 print OUT $first_row->{$key};
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
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282 print OUT "\t" if ++$counter < scalar(@keys);
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
283 }
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
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284 print OUT "\n";
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
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285 }
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
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286
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
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287 } elsif ($output_format eq "json"){
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
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288 my @result = toJSON($result);
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
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289
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
290 print OUT "[";
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
291 my $counter;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
292 foreach my $line (@result)
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
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293 {
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
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294 print OUT $line;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
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295 print OUT "," if ++$counter < scalar(@result);
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
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296 }
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
diff changeset
297 print OUT "]";
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
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298
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
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299 }
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
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300 close OUT;
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
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301 print "Results saved to '$output_file'\n";
a3b26189fee3 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
earlhaminst
parents:
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302 }