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1 #!/usr/bin/perl -w
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2
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3 =head1 NAME
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4
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5 seqlogo - runs the logo creation script
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6
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7 =head1 SYNOPSIS
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8
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9 seqlogo [OPTION]...-f [FILENAME]
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10
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11 =head1 DESCRIPTION
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12
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13 Creates a logo for the given input filename.
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14
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15 Available options:
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16 -B <bar bits> Number of bits in bar (real between 0, 1)
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17 -T <tic bits> Number of bits between tic marks
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18 -C <chars per line> Number of characters per line of logo
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19 -d <box shrink factor> Shrink factor of characters if option c is toggled
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20 -E <error bar fraction> Fraction of error bar to show (real between 0, 1 )
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21 -f <input file> Input filename
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22 -F <format> Format of output (EPS, GIF, PDF, PNG), - for STDOUT
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23 -h <logo height> Height of output logo (real > 0)
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24 -k <kind of data> 0 for amino acid, 1 for nucleic acid ; if not
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25 defined, a 90% certainty method is used to
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26 determine whether the input data is amino acid or
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27 nucleic acid
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28 -l <sequence lower bound> Lower bound of sequence (integer)
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29 -m <sequence upper bound> Upper bound of sequence (integer)
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30 -o <output file> Name of output file
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31 -s <sequence start> Sequence start number, defaults to 1 (int)
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32 -t <titletext> Text of title, enclosed in "" if more than one word
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33 -w <logo width> Width of output logo
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34 -x <x-axis label> Label for x-axis
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35 -y <y-axis label> Label for y-axis
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36
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37 Available toggles (no values associated)
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38 -a Toggle antialiasing
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39 -b Toggle bar ends
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40 -c Toggle color
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41 -e Toggle error bar
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42 -M Toggle small sample correction
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43 -O Toggle outlining of characters
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44 -n Toggle numbering of x-axis
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45 -S Toggle stretching of logos to entire length
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46 -X Toggle boxing of characters
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47 -Y Toggle y-axis
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48
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49 =head1 EXAMPLE
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50
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51 The following command takes as input "input.fasta" and returns the logo in the
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52 form "logo.eps". Antialiasing, bar ends, color, small sample correction,
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53 numbering of x-axis, and y-axis labelling are turned on:
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54
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55 seqlogo -f input.fasta -F EPS -o logo.eps -abcMnY
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56
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57 =cut
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58
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59 use vars qw($PATH);
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60
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61 BEGIN {
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62
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63 use FindBin qw($Bin);
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64 use lib "$Bin";
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65
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66 $PATH = $Bin;
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67
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68 ## $PATH = "/h/gary/Seqlogo/Code/";
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69 # $PATH = "/n/weblogo/home/httpd/weblogo/pub/beta/Seqlogo/Code";
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70 # unshift(@INC, $PATH);
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71 }
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72
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73 use logo;
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74 use template;
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75 use Getopt::Std;
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76 use FileHandle;
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77
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78
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79 my $opts;
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80 $opts =
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81 $opt_a || # antialiasing
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82 $opt_b || # bar ends (0 or 1)
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83 $opt_c || # color
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84 $opt_e || # show error bar (0 or 1)
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85 $opt_n || # numbering (0 or 1)
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86 $opt_M || # small sample correction (0 or 1)
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87 $opt_O || # outline (0 or 1)
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88 $opt_S || # stretch
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89 $opt_X || # box (0 for no box, 1 for box)
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90 $opt_Y || # y axis
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91
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92 $opt_B || # bar bits (real)
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93 $opt_T || # tics bits (real)
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94 $opt_C || # chars per line
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95 $opt_d || # box shrinking factor (<1)
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96 $opt_E || # error bar fraction (real)
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97 $opt_f || # input filename
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98 $opt_F || # format (PNG, EPS, PDF, GIF)
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99 $opt_h || # logo height (cm)
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100 $opt_k || # 0 = amino acid, 1 = nucleic acid
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101 $opt_l || # lower bound of sequence to put in logo
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102 $opt_m || # max bound of sequence to put in logo
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103 $opt_o || # output file
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104 $opt_s || # start number for very beginning of sequence
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105 $opt_t || # title text (string)
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106 $opt_w || # logo width (cm)
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107 $opt_x || # x axis label
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108 $opt_y || # y axis label
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109 $opts;
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110
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111 ################################################################################
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112 ##### USAGE #####
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113 ################################################################################
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114
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115 sub usage {
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116 my $usage = <<END
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117
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118 usage: seqlogo -f <input filename> [OPTIONs with values]
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119 Creates a logo for the given input filename.
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120
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121 Available options:
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122 -B <bar bits> Number of bits in bar (real # > 0)
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123 -T <tic bits> Number of bits between tic marks
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124 -C <chars per line> Number of characters per line of logo
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125 -d <box shrink factor> Shrink factor of characters if option c is toggled
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126 -E <error bar fraction> Fraction of error bar to show (real # > 0)
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127 -f <input filename> Input filename
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128 -F <format> Format of output (EPS, GIF, PDF, PNG), - for STDOUT
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129 -h <logo height> Height of output logo (real # > 0)
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130 -k <kind of data> 0 for amino acid, 1 for nucleic acid
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131 -l <sequence lower bound> Lower bound of sequence (integer)
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132 -m <sequence upper bound> Upper bound of sequence (integer)
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133 -o <output file> Name of output file
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134 -s <sequence start> Sequence start number, defaults to 1 (int)
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135 -t <titletext> Text of title, enclosed in "" if more than one word
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136 -w <logo width> Width of output logo
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137 -x <x-axis label> Label for x-axis
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138 -y <y-axis label> Label for y-axis
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139
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140 Available toggles (no values associated) bOenc
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141 -a Toggle antialiasing
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142 -b Toggle bar ends
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143 -c Toggle color
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144 -e Toggle error bar
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145 -M Toggle small sample correction
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146 -O Toggle outlining of characters
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147 -p Toggle fineprint
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148 -n Toggle numbering of x-axis
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149 -S Toggle stretching of logos to entire length
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150 -X Toggle boxing of characters
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151 -Y Toggle y-axis
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152
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153 END
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154 ;
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155
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156 return $usage;
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157 }
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158
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159 ################################################################################
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160 ##### MAIN FUNCTION #####
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161 ################################################################################
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162
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163 # arguments : $_[0] : file name
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164 MAIN: {
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165 init();
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166
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167 # feed data from file to make height data array reference
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168 my @input = <INPUTFILE>;
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169 close (INPUTFILE);
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170 my %heightparams = (
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171 smallsampletoggle => $opt_M,
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172 input_kind => $opt_k,
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173 stretch => $opt_S
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174 );
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175
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176 my ($heightdata_r, $desc_r, $kind, $goodlength, $badline, $validformat) =
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177 logo::getHeightData(\@input, \%heightparams);
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178
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179 # check for errors
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180 if ((defined $validformat) && ($validformat == 1)) {
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181 die("Error: Invalid input format does not conform to FASTA, " .
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182 "CLUSTAL, or Flat.\n");
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183 }
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184 if (!$goodlength) {
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185 die("Error: Number of characters in each logo line is not " .
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186 "consistent, starting at: ", $badline, "\n");
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187 }
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188
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189 my %input = (
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190 LOGO_HEIGHT => $opt_h,
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191 LOGO_WIDTH => $opt_w,
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192 COLORSCHEME => ($opt_c) ? "DEFAULT" : "BW",
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193
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194 LOGOSTART => $opt_l,
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195 LOGOEND => $opt_m,
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196 START_NUM => $opt_s,
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197
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198 TITLETEXT => $opt_t,
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199 YAXIS_LABEL => $opt_y,
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200 XAXIS_LABEL => $opt_x,
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201
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202 BOXSHRINK => $opt_d,
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203 CHARSPERLINE => $opt_C,
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204 BARBITS => $opt_B,
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205 TICBITS => $opt_T,
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206 RES => "96",
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207 "FORMAT" => (uc $opt_F),
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208
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209 # toggles
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210 ANTIALIAS => $opt_a,
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211 ERRBAR => $opt_e,
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212 FINEPRINT => $opt_p,
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213 NUMBERING => $opt_n,
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214 OUTLINE => $opt_O,
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215 SHOWENDS => $opt_b,
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216 SHOWINGBOX => $opt_X,
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217 YAXIS => $opt_Y
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218 );
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219
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220 template::create_template(\%input, $kind, $desc_r, $heightdata_r, $opt_o, $PATH);
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221 }
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222
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223
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224 ################################################################################
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225 ##### FUNCTINOS FOR INIT #####
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226 ################################################################################
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227
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228 # all ints
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229 sub isInt {
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230 return ($_[0] =~ /^[\+\-]?\d+$/) ? 1 : 0;
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231 }
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232
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233 # all reals
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234 sub isReal {
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235 return ($_[0] =~ /^[\+\-]?\d*.\d*?$/) ? 1 : 0;
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236 }
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237
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238 sub isZeroOrOne {
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239 return ($_[0] == 0 || $_[0] == 1) ? 1 : 0;
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240 }
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241
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242 sub init {
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243
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244 # if (not defined $PATH) {
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245 # die ("PATH must be defined\n");
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246 # } elsif (not -e $PATH) {
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247 # die ("PATH ($PATH) must exist\n");
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248 # } elsif (not -d $PATH) {
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249 # die ("PATH ($PATH) must be a directory\n");
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250 # }
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251
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252 &getopts('T:B:C:d:E:f:F:h:k:l:m:o:s:t:w:x:y:abcenMOpSXY');
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253
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254 if (defined $opt_B &&
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255 (!isReal($opt_B) || $opt_B < 0) ) {
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256 printf("\noption B must be a positive real, but is $opt_B, $!\n");
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257 die &usage();
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258 }
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259 if (defined $opt_d &&
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260 ( !isReal($opt_d) || $opt_d < 0 || $opt_d > 1) ) {
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261 print("\noption d must be a real between 0 and 1, but is $opt_d, $!\n");
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262 die &usage();
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263 }
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264 if (defined $opt_E &&
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265 (!isReal($opt_E) || $opt_E < 0 || $opt_E > 1) ) {
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266 print("\noption E must be a real between 0 and 1, but is $opt_E, $!\n");
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267 die &usage();
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268 }
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269 if (defined $opt_f) {
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270 open (INPUTFILE, "$opt_f") or die "Couldn't open input filename $opt_f: $!\n";
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271 } else {
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272 print("\ninput file not specified, terminating...\n");
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273 die &usage();
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274 }
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275 if (defined $opt_h &&
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276 (!isReal($opt_h) || $opt_h < 0) ) {
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277 print("\noption h must be a positive real, but is $opt_h, $!\n");
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278 die &usage();
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279 }
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280 if (defined $opt_w &&
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281 (!isReal($opt_w) || $opt_w < 0) ) {
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282 print("\noption w must be a positive real, but is $opt_w, $!\n");
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283 die &usage();
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284 }
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285 if (defined $opt_k &&
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286 (!isZeroOrOne($opt_k)) ) {
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287 print("\noption k must be 0 or 1, but is $opt_k, $!\n");
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288 die &usage();
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289 }
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290
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291 #toggles
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292 if (!defined $opt_a) {
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293 $opt_a = 0;
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294 }
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295 if (!defined $opt_b) {
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296 $opt_b = 0;
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297 }
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298 if (!defined $opt_c) {
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299 $opt_c = 0;
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300 }
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301 if (!defined $opt_e) {
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302 $opt_e = 0;
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303 }
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304 if (!defined $opt_n) {
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305 $opt_n = 0;
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306 }
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307 if (!defined $opt_M) {
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308 $opt_M = 0;
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309 }
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310 if (!defined $opt_O) {
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311 $opt_O = 0;
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312 }
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313 if (!defined $opt_p) {
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314 $opt_p = 0;
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315 }
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316 if (!defined $opt_S) {
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317 $opt_S = 0;
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318 }
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319 if (!defined $opt_X) {
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320 $opt_X = 0;
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321 };
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322 if (!defined $opt_Y) {
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323 $opt_Y = 0;
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324 };
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325
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326 if (!defined $opt_F) {
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327 $opt_F = "EPS"; # default to EPS
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328 }
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329 if (!defined $opt_o) {
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330 $opt_o = "-"; # for standard out
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331 } else {
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332 # $opt_o =~ s/\.\S*$//; # remove extension if there is one
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333 $opt_o .= "." . (lc $opt_F); # make file name
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334 }
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335
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336 if (defined $opt_C &&
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337 (!isInt($opt_C) || $opt_C < 0) ) {
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338 printf("\noption C must be a postive integer, but is $opt_C, $!\n");
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339 die &usage();
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340 }
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341
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342 if (defined $opt_l && !isInt($opt_l)) {
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343 printf("\noption l must be an integer, but is $opt_l, $!\n");
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344 die &usage();
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345 }
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346
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347 if (defined $opt_m && !isInt($opt_m)) {
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348 printf("\noption m must be an integer, but is $opt_m, $!\n");
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349 die &usage();
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350 }
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351
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352 if (defined $opt_s && !isInt($opt_s)) {
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353 printf("\noption s must be an integer, but is $opt_s, $!\n");
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354 die &usage();
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355 }
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356 }
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