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1 #!/usr/bin/perl -w
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2
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3 use strict;
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4 my $d_file="/home/inmare/galaxy/tools/pfam_annot/pfamA.txt";
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5 open(IN,$d_file);
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6 my %decode=();
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7 my %clan_decode;
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8 my $id="";
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9 my %c=();
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10
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11
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12 my $prot_file=shift;
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13 my $pfam_file=shift;
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14 my $prefix=shift;
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15
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16 while(<IN>)
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17 {
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18 if ($_=~/^\d/)
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19 {
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20 my @vl=(split(/\t+/));
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21 $decode{$vl[1]}="$vl[3]<br>";#$vl[8] $vl[9]";
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22 my $cc=0;
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23 my %repeated=();
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24 foreach my $v (@vl)
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25 {
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26 $v=~s/\[\d+\]/ /g;
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27 last if $v=~/hmmbuild/;
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28 last if $cc>10;
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29 next if $v=~/anon/;
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30 next if $v=~/Bates/;
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31 next if $v=~/Cogis/;
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32 next if $v=~/Coggis/;
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33 next if $v=~/Bateman/;
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34 next if $v=~/Sonnhammer/;
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35 next if $v=~/Finn/;
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36 next if $v=~/Studholme/;
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37 next if $v=~/Kerrison/;
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38 next if $repeated{$v};
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39 next if $v eq $vl[3];
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40 next unless length($v)>=20 && $cc<=9;
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41 $decode{$vl[1]}.="$v ";
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42 $repeated{$v}++;
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43 $cc++;
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44 }
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45 #print "$vl[1] $decode{$vl[1]}\n";
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46 }
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47 }
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48 close(IN);
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49
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50 my $clan_file="/home/inmare/galaxy/tools/pfam_annot/clans.txt";
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51 open(IN,$clan_file);
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52 while(<IN>)
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53 {
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54 my @vl=(split(/\t/));
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55 #$clan_decode{$vl[1]}="$vl[3]";
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56 my $cc=0;
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57 foreach my $v (@vl)
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58 {
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59 $cc++;
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60 $v=~s/\[\d+\]/ /g;
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61 $clan_decode{$vl[1]}.="$v " if length($v) >=30 && $cc<=10;
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62 }
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63
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64 }
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65 my %plasm=();
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66 open(IN,"$prot_file");
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67 while(<IN>)
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68 {
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69 if ($_=~/^>(.*)/)
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70 {
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71 $id=$1;
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72 $id=(split(/\s+/,$id))[0];
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73 if ($id=~/#/)
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74 {
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75 my $pid=(split(/\#/,$id))[0];
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76 $plasm{$pid}++;
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77 }
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78 }else{
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79 chomp;
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80 $c{$id}.=$_;
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81 }
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82 }
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83 close(IN);
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84
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85 open(OUT,">$prefix");
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86 print OUT "<html>\n<head>\n";
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87 print OUT "<style type=\"text/css\">\nspan {\n\ttext-decoration:underline;\n\tcolor:blue;\n\tcursor:pointer;\n}\n</style>\n";
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88 print OUT "<script>\nfunction show(elementID) {\n\tvar ele = document.getElementById(elementID);\n\tif (!ele) {\n\t\talert(\"no such element\");\t\treturn;\n\t}\n\tvar pages = document.getElementsByClassName('page');\n\tfor(var i = 0; i < pages.length; i++) {\n\t\tpages[i].style.display = 'none';\n\t}\n\tele.style.display = 'block';\n}\n</script>\n";
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89 #print OUT "<script src=\"script.js\"></script>\n";
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90 #print OUT "<script>\n\tshow(elementID)\n</script>\n";
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91 print OUT "</head>\n";
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92 my $color="\"#czb9dz\"";
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93 my %printed;
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94 open(IN,$pfam_file);
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95 print OUT "Proteins with PFAM domains:\n<br><br>\n";
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96 my @dd=keys %plasm;
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97 if ($#dd>0)
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98 {
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99 print OUT "<p>Show results ";
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100 for (my $i=0;$i<=$#dd;$i++)
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101 {
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102 if ($i==$#dd)
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103 {
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104 print OUT "<span onclick=\"show(\'$dd[$i]\');\">$dd[$i]</span>.</p>\n";
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105 }else{
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106 print OUT "<span onclick=\"show(\'$dd[$i]\');\">$dd[$i]</span>,\n";
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107 }
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108 }
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109 }else{
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110 print OUT "<div>\n<table cellpadding=\"0\" width=650>\n"; #div per ogni plasmide|
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111 }
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112 my $ntokens=0;
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113 my $prev_plasmid="";
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114 my $curr_plasmid="";
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115 my $np=0;
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116 while(<IN>)
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117 {
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118 next if $_=~/^\#/;
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119 my ($name,$domain,$clan)=(split(/\s+/))[0,5,-1];
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120 next unless $name;
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121 if ($name=~/#/)
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122 {
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123 $curr_plasmid=(split(/\#/,$name))[0];
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124 if ($curr_plasmid ne $prev_plasmid)
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125 {
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126 if ($np>0)
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127 {
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128 print OUT "</table>\n";
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129 print OUT "</div>\n";
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130 }
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131 print OUT "<div id=\"$curr_plasmid\" class=\"page\" style=\"\">\n";
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132 print OUT "<table cellpadding=\"0\" width=650>\n";
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133 $np++;
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134 }
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135 $prev_plasmid=$curr_plasmid;
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136 }
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137
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138 $domain=~s/\.\d+//;
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139 unless ($printed{$name})
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140 {
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141 my $seq=$c{$name};
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142
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143 $seq=~s/\*//g;
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144 $seq=form($seq,90);
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145 print OUT "<td>\n";
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146 print OUT "<HR SIZE=3 WIDTH=80%></HR>\n";
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147 print OUT "<center><b>$name</b><br>\n</center>\n";
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148 print OUT "</td>\n<tr></tr>\n";
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149 print OUT "<td bgcolor=$color>\n";
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150 print OUT "<pre> \n$seq\n </pre>\n";
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151 print OUT "</td>\n<tr></tr>\n<td></td>\n<tr></tr>\n";
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152 $ntokens=2;
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153 }
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154 my $hd=uc $domain;
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155 #<a href="http://www.canoro.altervista.org/" class="nav" target="_blank">www.canoro.altervista.org</a>
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156 if ($decode{$domain})
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157 {
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158 my $ddes=$decode{$domain};
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159 $ddes=~s/\s+/ /g;
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160 if ($ntokens % 2==0)
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161 {
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162 print OUT "<td>\n";
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163 }else{
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164 print OUT "<td bgcolor=$color>\n";
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165 }
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166
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167 print OUT "<p align=\"left\">\n";
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168 print OUT "<a href=http://pfam.xfam.org/family/$hd> $domain</a>\n<p align=\"justify\">$ddes</p>\n\n";
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169 print OUT "</p>\n</td>\n<tr></tr>\n<td></td>\n<tr></tr>\n";
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170 $ntokens++;
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171 }
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172 if ($clan_decode{$clan})
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173 {
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174 my $clanD=$clan_decode{$clan};
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175 $clanD=~s/\s+/ /g;
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176 next if $decode{$domain} eq $clan_decode{$clan};
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177 my $ddes=$decode{$domain};
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178 if ($ntokens % 2==0)
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179 {
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180 print OUT "<td>\n";
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181 }else{
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182 print OUT "<td bgcolor=$color>\n";
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183 }
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184
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185 print OUT "<p align=\"left\">\n";
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186 print OUT "<a href=http://pfam.xfam.org/clan/$clan> $clan</a>\n <p align=\"justify\">$clanD</p>\n\n";
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187 print OUT "</p>\n</td>\n<tr></tr>\n<td></td>\n<tr></tr>\n";
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188 $ntokens++;
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189 }
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190 $printed{$name}=1;
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191 }
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192
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193 #if ($curr_plasmid ne "")
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194 #{
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195 print OUT "</table>\n";
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196 print OUT "</div>\n";
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197 print OUT "</body>\n";
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198 #}
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199 #print OUT "<br><br>Proteins without PFAM domains:\n<br>\n";
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200 #foreach my $seq (keys %c)
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201 #{
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202 # next if $printed{$seq};
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203 # print OUT "<>$seq</pre>\n\n<br><br><left>\n$c{$seq}</left><br>\n";
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204 # print OUT "<HR SIZE=3 WIDTH=80%>\n";
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205 #}
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206 #print OUT "</table>\n</div>\n</body>\n</html>\n";
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207 #close(OUT);
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208
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209 sub form
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210 {
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211 my $string=$_[0];
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212 my $len=$_[1];
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213 my $outS="";
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214 for (my $i=0;$i<=length($string);$i+=$len)
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215 {
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216 $outS.=substr($string,$i,$len)."\n";
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217 }
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218 #print "A:$outS";
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219 #$outS=~s/\s+//g;
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220 return $outS;
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221 }
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