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annotate lib/csv.pm @ 0:023c380900ef draft default tip
Init repository with last massbank_ws_searchspectrum master version
author | fgiacomoni |
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date | Wed, 19 Apr 2017 11:31:58 -0400 |
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Init repository with last massbank_ws_searchspectrum master version
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1 package lib::csv ; |
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2 |
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3 use strict; |
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4 use warnings ; |
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5 use Exporter ; |
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6 use Carp ; |
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7 |
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8 use Text::CSV ; |
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9 |
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10 use Data::Dumper ; |
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11 |
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12 use vars qw($VERSION @ISA @EXPORT %EXPORT_TAGS); |
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13 |
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14 our $VERSION = "1.0"; |
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15 our @ISA = qw(Exporter); |
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16 our @EXPORT = qw( get_csv_object get_value_from_csv get_value_from_csv_multi_header ); |
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17 our %EXPORT_TAGS = ( ALL => [qw( get_csv_object get_value_from_csv get_value_from_csv_multi_header )] ); |
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18 |
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19 =head1 NAME |
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20 |
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21 My::Module - An example module |
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22 |
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23 =head1 SYNOPSIS |
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24 |
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25 use My::Module; |
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26 my $object = My::Module->new(); |
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27 print $object->as_string; |
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28 |
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29 =head1 DESCRIPTION |
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30 |
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31 This module does not really exist, it |
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32 was made for the sole purpose of |
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33 demonstrating how POD works. |
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34 |
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35 =head1 METHODS |
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36 |
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37 Methods are : |
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38 |
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39 =head2 METHOD new |
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40 |
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41 ## Description : new |
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42 ## Input : $self |
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43 ## Ouput : bless $self ; |
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44 ## Usage : new() ; |
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45 |
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46 =cut |
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47 |
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48 sub new { |
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49 ## Variables |
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50 my $self={}; |
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51 bless($self) ; |
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52 return $self ; |
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53 } |
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54 ### END of SUB |
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55 |
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56 =head2 METHOD get_csv_object |
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57 |
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58 ## Description : builds a csv object and etablishes format |
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59 ## Input : $separator |
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60 ## Output : $csv |
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61 ## Usage : my ( $csv ) = get_csv_object( $separator ) ; |
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62 |
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63 =cut |
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64 ## START of SUB |
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65 sub get_csv_object { |
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66 ## Retrieve Values |
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67 my $self = shift ; |
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68 my ( $separator ) = @_ ; |
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69 |
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70 # my $csv = Text::CSV->new({'sep_char' => "$separator"}); |
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71 my $csv = Text::CSV->new ( {'sep_char' => "$separator", binary => 1, } ) # should set binary attribute. |
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72 or die "Cannot use CSV: ".Text::CSV->error_diag (); |
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73 |
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74 return($csv) ; |
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75 } |
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76 ## END of SUB |
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77 |
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78 =head2 METHOD get_value_from_csv |
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79 |
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80 ## Description : extract a targeted column in a csv file |
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81 ## Input : $csv, $file, $column, $is_header |
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82 ## Output : $value |
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83 ## Usage : my ( $value ) = get_value_from_csv( $csv, $file, $column, $is_header ) ; |
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84 |
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85 =cut |
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86 ## START of SUB |
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87 sub get_value_from_csv { |
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88 ## Retrieve Values |
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89 my $self = shift ; |
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90 my ( $csv, $file, $column, $is_header ) = @_ ; |
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91 |
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92 my @value = () ; |
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93 |
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94 ## Adapte the number of the colunm : (nb of column to position in array) |
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95 $column = $column - 1 ; |
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96 |
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97 open (CSV, "<", $file) or die $! ; |
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98 |
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99 my $line = 0 ; |
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100 |
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101 while (<CSV>) { |
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102 $line++ ; |
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103 chomp $_ ; |
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104 # file has a header |
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105 if ( defined $is_header ) { if ($line == 1) { next ; } } |
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106 # parsing the targeted column |
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107 if ( $csv->parse($_) ) { |
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108 my @columns = $csv->fields(); |
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109 push ( @value, $columns[$column] ) ; |
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110 } |
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111 else { |
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112 my $err = $csv->error_input; |
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113 die "Failed to parse line: $err"; |
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114 } |
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115 } |
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116 close CSV; |
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117 return(\@value) ; |
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118 } |
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119 ## END of SUB |
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120 |
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121 =head2 METHOD get_value_from_csv_multi_header |
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122 |
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123 ## Description : extract a targeted column in a csv file |
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124 ## Input : $csv, $file, $column, $is_header, $nb_header |
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125 ## Output : $value |
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126 ## Usage : my ( $value ) = get_value_from_csv_multi_header( $csv, $file, $column, $is_header, $nb_header ) ; |
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127 |
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128 =cut |
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129 ## START of SUB |
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130 sub get_value_from_csv_multi_header { |
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131 ## Retrieve Values |
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132 my $self = shift ; |
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133 my ( $csv, $file, $column, $is_header, $nb_header ) = @_ ; |
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134 |
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135 my @value = () ; |
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136 |
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137 ## Adapte the number of the colunm : (nb of column to position in array) |
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138 $column = $column - 1 ; |
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139 |
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140 open (CSV, "<", $file) or die $! ; |
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141 |
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142 my $line = 0 ; |
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143 |
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144 while (<CSV>) { |
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145 $line++ ; |
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146 chomp $_ ; |
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147 # file has a header |
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148 if ( defined $is_header and $is_header eq 'yes') { if ($line <= $nb_header) { next ; } } |
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149 # parsing the targeted column |
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150 if ( $csv->parse($_) ) { |
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151 my @columns = $csv->fields(); |
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152 my $value = $columns[$column] ; |
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153 $value =~s/\r|\n// ; |
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154 push ( @value, $value ) ; |
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155 } |
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156 else { |
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157 my $err = $csv->error_input; |
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158 die "Failed to parse line: $err"; |
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159 } |
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160 } |
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161 close CSV; |
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162 return(\@value) ; |
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163 } |
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164 ## END of SUB |
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165 |
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166 =head2 METHOD parse_csv_object |
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167 |
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168 ## Description : parse_all csv object and return a array of rows |
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169 ## Input : $csv, $file |
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170 ## Output : $csv_matrix |
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171 ## Usage : my ( $csv_matrix ) = parse_csv_object( $csv, $file ) ; |
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172 |
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173 =cut |
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174 ## START of SUB |
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175 sub parse_csv_object { |
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176 ## Retrieve Values |
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177 my $self = shift ; |
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178 my ( $csv, $file ) = @_ ; |
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179 |
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180 my @csv_matrix = () ; |
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181 |
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182 open my $fh, "<:encoding(utf8)", $$file or die "Can't open csv file $$file: $!"; |
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183 |
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184 while ( my $row = $csv->getline( $fh ) ) { |
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185 push @csv_matrix, $row; |
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186 } |
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187 $csv->eof or $csv->error_diag(); |
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188 close $fh; |
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189 |
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190 return(\@csv_matrix) ; |
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191 } |
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192 ## END of SUB |
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193 |
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194 =head2 METHOD parse_allcsv_object |
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195 |
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196 ## Description : parse_all csv object and return a array of rows with or without header |
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197 ## Input : $csv, $file, $keep_header |
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198 ## Output : $csv_matrix |
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199 ## Usage : my ( $csv_matrix ) = parse_csv_object( $csv, $file, $keep_header ) ; |
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200 |
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201 =cut |
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202 ## START of SUB |
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203 sub parse_allcsv_object { |
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204 ## Retrieve Values |
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205 my $self = shift ; |
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206 my ( $csv, $file, $keep_header ) = @_ ; |
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207 |
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208 my @csv_matrix = () ; |
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209 my $line = 1 ; |
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210 |
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211 open my $fh, "<:encoding(utf8)", $$file or die "Can't open csv file $$file: $!"; |
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212 |
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213 while ( my $row = $csv->getline( $fh ) ) { |
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214 if ( ( $keep_header eq 'n' ) and ($line == 1) ) { } |
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215 else { push @csv_matrix, $row; } |
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216 $line ++ ; |
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217 } |
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218 my $status = $csv->eof or $csv->error_diag(); |
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219 close $fh; |
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220 |
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221 return(\@csv_matrix, $status) ; |
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222 } |
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223 ## END of SUB |
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224 |
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225 |
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226 =head2 METHOD write_csv_from_arrays |
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227 |
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228 ## Description : write a csv file from list of rows |
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229 ## Input : $csv, $file_name, $rows |
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230 ## Output : $csv_file |
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231 ## Usage : my ( $csv_file ) = write_csv_from_arrays( $csv, $file_name, $rows ) ; |
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232 |
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233 =cut |
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234 ## START of SUB |
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235 sub write_csv_from_arrays { |
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236 ## Retrieve Values |
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237 my $self = shift ; |
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238 my ( $csv, $file_name, $rows ) = @_ ; |
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239 |
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240 my $fh = undef ; |
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241 $csv->eol ("\n"); ## end-of-line string to add to rows |
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242 $csv->quote_char(undef) ; |
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243 open $fh, ">:encoding(utf8)", "$file_name" or die "$file_name: $!"; |
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244 |
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245 my $status = $csv->print ($fh, $_) for @{$rows}; |
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246 close $fh or die "$file_name: $!"; |
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247 |
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248 return(\$file_name) ; |
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249 } |
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250 ## END of SUB |
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251 |
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252 1 ; |
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253 |
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254 |
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255 __END__ |
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256 |
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257 =head1 SUPPORT |
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258 |
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259 You can find documentation for this module with the perldoc command. |
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260 |
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261 perldoc csv.pm |
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262 |
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263 =head1 Exports |
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264 |
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265 =over 4 |
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266 |
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267 =item :ALL is get_csv_object, get_value_from_csv |
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268 |
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269 =back |
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270 |
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271 =head1 AUTHOR |
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272 |
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273 Franck Giacomoni E<lt>franck.giacomoni@clermont.inra.frE<gt> |
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274 |
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275 =head1 LICENSE |
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276 |
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277 This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself. |
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278 |
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279 =head1 VERSION |
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280 |
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281 version 1 : 23 / 10 / 2013 |
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282 |
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283 version 2 : ?? |
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284 |
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285 =cut |