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annotate libs/sratoolkit.2.8.0-centos_linux64/example/perl/gene-lookup.pl @ 3:38ad1130d077 draft

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planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
author charles_s_test
date Mon, 27 Nov 2017 11:21:07 -0500
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1 #!/usr/bin/env perl
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2 # ===========================================================================
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3 #
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4 # PUBLIC DOMAIN NOTICE
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5 # National Center for Biotechnology Information
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6 #
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7 # This software/database is a "United States Government Work" under the
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8 # terms of the United States Copyright Act. It was written as part of
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9 # the author's official duties as a United States Government employee and
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10 # thus cannot be copyrighted. This software/database is freely available
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11 # to the public for use. The National Library of Medicine and the U.S.
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12 # Government have not placed any restriction on its use or reproduction.
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13 #
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14 # Although all reasonable efforts have been taken to ensure the accuracy
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15 # and reliability of the software and data, the NLM and the U.S.
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16 # Government do not and cannot warrant the performance or results that
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17 # may be obtained by using this software or data. The NLM and the U.S.
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18 # Government disclaim all warranties, express or implied, including
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19 # warranties of performance, merchantability or fitness for any particular
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20 # purpose.
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21 #
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22 # Please cite the author in any work or product based on this material.
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23 #
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24 # ===========================================================================
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25
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26 use warnings;
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27 use LWP::Simple;
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28
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29 use Data::Dumper;
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30
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31 my %opts = (
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32 host => 'www.ncbi.nlm.nih.gov',
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33 cgi => 'projects/variation/tools/1000genomes/genomesearch.cgi',
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34 assm => 'GCF_000001405.17',
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35 filter => ''
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36 );
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37
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38 sub usage()
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39 {
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40 print <<"HELP";
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41 convert gene names to chromosome and range
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42
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43 Usage:
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44 $0 <name>...
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45 options are
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46 -h | -? | --help this message
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47
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48 Example:
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49 $0 williams
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50
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51 HELP
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52 exit 0;
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53 }
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54
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55 #@ARGV = ( 'cat' ) if scalar @ARGV == 0;
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56 usage if scalar @ARGV == 0;
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57 foreach (@ARGV) {
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58 usage() if (/^-h$/ || /^-\?$/ || /^--help$/);
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59 }
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60
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61 package JSON;
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62
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63 sub _json_object;
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64 sub _json_array;
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65 sub _json_value;
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66 sub _json_value_check;
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67
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68 use constant {
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69 cc_WHITESPACE => 1,
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70 cc_OPERATOR => 2,
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71 cc_QUOTE => 4,
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72 cc_ESCAPE => 8,
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73 cc_ESCAPED => 16,
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74 cc_UNICODED => 32
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75 };
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76
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77 my @CC = map {
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78 my $x = 0;
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79
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80 $x |= cc_WHITESPACE if (chr($_) =~ /\s/);
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81 $x |= cc_OPERATOR if (chr($_) =~ /[\[\]{},:]/);
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82 $x |= cc_QUOTE if (chr($_) eq '"');
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83 $x |= cc_ESCAPE if (chr($_) eq '\\');
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84 $x |= cc_ESCAPED if (chr($_) =~ /[\\\/bfnrt]/);
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85 $x |= cc_UNICODED if (chr($_) eq 'u');
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86 $x;
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87 } (0..255);
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88
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89 sub _json_token_string
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90 {
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91 my ($sref, $i) = @_;
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92 my $slen = length($$sref);
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93 my $st = 1;
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94 my $string = '';
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95
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96 for ( ; $$i < $slen; ++$$i) {
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97 local $_ = substr($$sref, $$i, 1);
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98 my $cc = $CC[ord($_)];
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99
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100 if ($st == 1) { # string tokenizing
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101 if ($cc & cc_QUOTE) {
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102 ++$$i;
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103 return ('string', eval "\"$string\"")
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104 }
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105 if ($cc & cc_ESCAPE) {
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106 ++$st;
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107 }
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108 else {
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109 $string .= $_;
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110 }
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111 next;
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112 }
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113 if ($st == 2) { # escape tokenizing
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114 if ($cc & cc_ESCAPED) {
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115 $string .= "\\$_";
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116 }
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117 elsif ($cc & cc_UNICODED) {
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118 my $value = substr($$sref, $$i + 1, 4);
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119
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120 return (undef, 'expected 4 hex digits') unless $value =~ /[[:xdigit:]]{4}/;
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121 $string .= "\\N{U+$value}";
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122 $$i += 4;
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123 }
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124 else {
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125 $string .= "\\\\$_";
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126 }
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127 $st = 1;
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128 next;
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129 }
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130 }
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131 }
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132
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133 sub _json_token
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134 {
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135 my ($sref, $i) = @_;
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136 my $slen = length($$sref);
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137
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138 for ( ; $$i < $slen; ++$$i) {
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139 local $_ = substr($$sref, $$i, 1);
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140 my $cc = $CC[ord($_)];
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141
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142 next if ($cc & cc_WHITESPACE);
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143
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144 if ($cc & cc_QUOTE) {
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145 ++$$i;
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146 return _json_token_string(@_);
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147 }
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148 if ($cc & cc_OPERATOR) {
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149 ++$$i;
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150 return ('op', $_);
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151 }
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152 if (substr($$sref, $$i, 5) eq 'false') {
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153 $$i += 5;
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154 return ('bool', 0);
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155 }
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156 if (substr($$sref, $$i, 4) eq 'true') {
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157 $$i += 4;
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158 return ('bool', 1);
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159 }
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160 if (substr($$sref, $$i, 4) eq 'null') {
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161 $$i += 4;
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162 return ('null', undef);
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163 }
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164 if (substr($$sref, $$i) =~ /^(-{0,1}\d+(?:\.\d+){0,1}(?:e[-+]{0,1}\d+){0,1})/i) {
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165 my $value = $1;
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166
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167 $$i += length $value;
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168 return ('number', eval $value);
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169 }
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170 substr($$sref, $$i) =~ /(\w+)/;
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171 return (undef, "unexpected '$1'");
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172 }
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173 return ('empty', 'no input');
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174 }
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175
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176 sub _json_value
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177 {
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178 my $start = ${$_[1]};
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179 my ($type, $value) = _json_token(@_);
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180 my $len = ${$_[1]} - $start;
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181
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182 $len = 10 if $len < 10;
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183 die substr(${$_[0]}, $start, $len)."\nJSON syntax error: $value" unless $type;
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184 if ($type eq 'op') {
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185 if ($value eq '{') {
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186 $type = 'object';
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187 $value = _json_object(@_);
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188 }
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189 elsif ($value eq '[') {
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190 $type = 'array';
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191 $value = _json_array(@_);
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192 }
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193 }
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194 return ($type, $value);
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195 }
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196
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197 sub _json_value_check
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198 {
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199 my ($type, $value) = @_;
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200
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201 return $value if ( $type eq 'array'
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202 || $type eq 'bool'
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203 || $type eq 'null'
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204 || $type eq 'number'
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205 || $type eq 'object'
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206 || $type eq 'string');
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207
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208 die "JSON syntax error: expected array, bool, null, object, or string";
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209 }
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210
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211 sub _json_object
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212 {
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213 my $rslt;
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214
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215 for ( ; ; ) {
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216 my ($type, $value) = _json_token(@_);
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217 my $name;
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218
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219 unless (defined($rslt)) {
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220 $rslt = {};
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221 last if ($type eq 'op' && $value eq '}');
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222 }
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223 die "JSON syntax error: expected string" unless $type eq 'string';
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224 $name = $value;
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225
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226 ($type, $value) = _json_token(@_);
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227 die "JSON syntax error: expected ':', have '$value'" unless ($type eq 'op' && $value eq ':');
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228
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229 $rslt->{$name} = _json_value_check(_json_value(@_));
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230
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231 ($type, $value) = _json_token(@_);
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232 die "JSON syntax error: $value" unless defined($type);
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233 last if ($type eq 'op' && $value eq '}');
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234 die "JSON syntax error: expected ',' or '}', have '$value'" unless ($type eq 'op' && $value eq ',');
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235 }
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236 return $rslt;
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237 }
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238
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239 sub _json_array
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240 {
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241 my $rslt;
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242
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243 for ( ; ; ) {
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244 my ($type, $value) = _json_value(@_);
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245
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246 unless (defined($rslt)) {
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247 $rslt = [];
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248 last if ($type eq 'op' && $value eq ']');
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249 }
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250 push @{$rslt}, _json_value_check($type, $value);
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251
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252 ($type, $value) = _json_token(@_);
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253 last if ($type eq 'op' && $value eq ']');
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254 die "JSON syntax error: expected ',' or ']', have '$value'" unless ($type eq 'op' && $value eq ',');
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255 }
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256 return $rslt;
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257 }
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258
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259 sub decode()
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260 {
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261 my $self = $_[0];
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262 my $i = 0; # holds current parsing position
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263
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264 return _json_value_check(_json_value(\$self->{'source'}, \$i));
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265 }
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266
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267 sub new($)
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268 {
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269 my $class = $_[0];
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270 my $self = { 'source' => ($_[1] || '') };
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271
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272 bless $self, $class;
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273 return $self;
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274 }
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275
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276 package main;
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277
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278 sub get_object_locations($)
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279 {
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280 my $response = get("http://$opts{'host'}/$opts{'cgi'}?assm=$opts{'assm'}&query=$_[0]");
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281 my $json = new JSON($response);
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282 my $parsed = $json->decode();
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283
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284 return $parsed->{'results'}->{'obj_locs'};
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285 }
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286
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287 sub process($)
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288 {
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289 my $obj_locs = get_object_locations($_[0]);
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290
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291 foreach ( @{$obj_locs} ) {
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292 my $type = $_->{'feature_type'};
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293
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294 if (!$opts{'filter'} || $type eq $opts{'filter'}) {
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295 my $label = $_->{'label'};
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296 my $chrom = $_->{'chr'}->{'chrom'};
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297 my $from = $_->{'seq_from'};
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298 my $to = $_->{'seq_to'};
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299
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300 printf("%s: %s\tslice: '%s:%u-%u'\n",
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301 $type, $label, $chrom, $from, $to);
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302 }
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303 }
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304 }
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305
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306 for (my $i = 0; $i < scalar @ARGV; ++$i) {
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307 $_ = $ARGV[$i];
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308
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309 if (/^-/) {
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310 if (/^--filter/) {
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311 $opts{'filter'} = $ARGV[++$i];
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312 next;
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313 }
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314 if (/^--assembly/) {
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315 $opts{'assm'} = $ARGV[++$i];
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316 next;
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317 }
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318 usage();
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319 }
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320 process $_;
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321 }