Mercurial > repos > fgiacomoni > hmdb_ms_search
annotate lib/csv.pm @ 18:ec7c05889e67 draft
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author | fgiacomoni |
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date | Wed, 23 Jan 2019 03:02:07 -0500 |
parents | 625fa968d99a |
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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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10 use Data::Dumper ; |
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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_multi_header ); |
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17 our %EXPORT_TAGS = ( ALL => [qw( get_csv_object get_value_from_csv_multi_header )] ); |
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18 |
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19 =head1 NAME |
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21 My::Module - An example module |
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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_multi_header |
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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, $nb_header |
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82 ## Output : $value |
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83 ## Usage : my ( $value ) = get_value_from_csv_multi_header( $csv, $file, $column, $is_header, $nb_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_multi_header { |
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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, $nb_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 and $is_header eq 'yes') { if ($line <= $nb_header) { 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 parse_csv_object |
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122 |
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123 ## Description : parse_all csv object and return a array of rows |
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124 ## Input : $csv, $file |
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125 ## Output : $csv_matrix |
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126 ## Usage : my ( $csv_matrix ) = parse_csv_object( $csv, $file ) ; |
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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 parse_csv_object { |
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131 ## Retrieve Values |
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132 my $self = shift ; |
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133 my ( $csv, $file ) = @_ ; |
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134 |
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135 my @csv_matrix = () ; |
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136 |
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137 open my $fh, "<:encoding(utf8)", $$file or die "Can't open csv file $$file: $!"; |
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138 |
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139 while ( my $row = $csv->getline( $fh ) ) { |
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140 push @csv_matrix, $row; |
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141 } |
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142 $csv->eof or $csv->error_diag(); |
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143 close $fh; |
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144 |
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145 return(\@csv_matrix) ; |
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146 } |
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147 ## END of SUB |
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148 |
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149 =head2 METHOD parse_allcsv_object |
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150 |
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151 ## Description : parse_all csv object and return a array of rows with or without header |
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152 ## Input : $csv, $file, $keep_header |
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153 ## Output : $csv_matrix |
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154 ## Usage : my ( $csv_matrix ) = parse_csv_object( $csv, $file, $keep_header ) ; |
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155 |
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156 =cut |
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157 ## START of SUB |
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158 sub parse_allcsv_object { |
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159 ## Retrieve Values |
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160 my $self = shift ; |
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161 my ( $csv, $file, $keep_header ) = @_ ; |
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162 |
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163 my @csv_matrix = () ; |
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164 my $line = 1 ; |
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165 |
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166 open my $fh, "<:encoding(utf8)", $$file or die "Can't open csv file $$file: $!"; |
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167 |
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168 while ( my $row = $csv->getline( $fh ) ) { |
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169 if ( ( $keep_header eq 'n' ) and ($line == 1) ) { } |
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170 else { push @csv_matrix, $row; } |
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171 $line ++ ; |
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172 } |
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173 my $status = $csv->eof or $csv->error_diag(); |
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174 close $fh; |
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175 |
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176 return(\@csv_matrix, $status) ; |
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177 } |
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178 ## END of SUB |
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179 |
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180 |
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181 =head2 METHOD write_csv_from_arrays |
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182 |
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183 ## Description : write a csv file from list of rows |
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184 ## Input : $csv, $file_name, $rows |
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185 ## Output : $csv_file |
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186 ## Usage : my ( $csv_file ) = write_csv_from_arrays( $csv, $file_name, $rows ) ; |
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187 |
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188 =cut |
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189 ## START of SUB |
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190 sub write_csv_from_arrays { |
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191 ## Retrieve Values |
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192 my $self = shift ; |
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193 my ( $csv, $file_name, $rows ) = @_ ; |
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194 |
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195 my $fh = undef ; |
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196 $csv->eol ("\n"); ## end-of-line string to add to rows |
14 | 197 # $csv->quote_char(undef) ; |
198 open $fh, ">:encoding(utf8)", "$file_name" or die "$file_name: $!"; | |
199 | |
200 my $status = $csv->print ($fh, $_) for @{$rows}; | |
201 close $fh or die "$file_name: $!"; | |
202 | |
203 return(\$file_name) ; | |
204 } | |
205 ## END of SUB | |
206 | |
207 | |
208 =head2 METHOD write_csv_from_hash | |
209 | |
210 ## Description : write a csv file from simple hash with headers | |
211 ## Input : $csv, $file_name, $headers, $arrayofhash | |
212 ## Output : $csv_file | |
213 ## Usage : my ( $csv_file ) = write_csv_from_arrays( $csv, $file_name, $headers, $arrayofhash ) ; | |
214 | |
215 =cut | |
216 ## START of SUB | |
217 sub write_csv_from_array_of_hash { | |
218 ## Retrieve Values | |
219 my $self = shift ; | |
220 my ( $csv, $file_name, $headers, $hash ) = @_ ; | |
221 | |
222 my $fh = undef ; | |
223 $csv->eol ("\n"); ## end-of-line string to add to rows | |
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224 $csv->quote_char(undef) ; |
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225 open $fh, ">:encoding(utf8)", "$file_name" or die "$file_name: $!"; |
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226 |
14 | 227 if (defined $headers) { |
228 for my $field (@$headers) { print $fh join('\t', $field), "\n"; } ; | |
229 } | |
230 | |
231 for my $row (keys %{$hash}) { | |
232 print $fh join('\t', map { $_, $row->{$_} } sort keys %$row), "\n"; | |
233 } | |
234 | |
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235 close $fh or die "$file_name: $!"; |
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236 |
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237 return(\$file_name) ; |
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238 } |
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239 ## END of SUB |
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240 |
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241 1 ; |
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242 |
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243 |
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244 __END__ |
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245 |
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246 =head1 SUPPORT |
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247 |
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248 You can find documentation for this module with the perldoc command. |
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249 |
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250 perldoc csv.pm |
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251 |
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252 =head1 Exports |
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253 |
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254 =over 4 |
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255 |
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256 =item :ALL is get_csv_object, get_value_from_csv_multi_header |
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257 |
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258 =back |
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259 |
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260 =head1 AUTHOR |
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261 |
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262 Franck Giacomoni E<lt>franck.giacomoni@clermont.inra.frE<gt> |
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263 |
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264 =head1 LICENSE |
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265 |
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266 This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself. |
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267 |
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268 =head1 VERSION |
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269 |
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270 version 1 : 23 / 10 / 2013 |
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271 |
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272 version 2 : ?? |
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273 |
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274 =cut |