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1 #!/usr/bin/perl -w
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2 #Filename:
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3 #Author: Tian Dongmei
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4 #Email: tiandm@big.ac.cn
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5 #Date: 2014-5-29
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6 #Modified:
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7 #Description:
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8 my $version=1.00;
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9
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10 use strict;
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11 use Getopt::Long;
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12 use File::Basename;
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13
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14 my %opts;
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15 GetOptions(\%opts,"i=s","format=s","min=i","max=i","o=s","h");
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16 if (!(defined $opts{o} and defined $opts{format} and defined $opts{i} ) || defined $opts{h}) { #necessary arguments
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17 &usage;
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18 }
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19 my ($config,$prepath,$rfampath,$knownpath,$genomepath,$novelpath);
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20 my ($predir,$rfamdir,$knowndir,$genomedir,$noveldir);
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21 open IN,"<$opts{i}";
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22 $config=<IN>; chomp $config;
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23 $prepath=<IN>; chomp $prepath;
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24 $genomepath=<IN>; chomp $genomepath;
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25 $rfampath=<IN>;
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26 close IN;
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27 my @tmp=split/\//,$prepath;
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28 $predir=$tmp[-1];
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29 @tmp=split/\//,$genomepath;
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30 $genomedir=$tmp[-1];
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31
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32 my $dir=dirname($opts{'o'});
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33
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34 open OUT ,">$opts{'o'}";
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35 print OUT "<HTML>\n <HEAD>\n <TITLE> Analysis Report </TITLE>\n </HEAD>
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36 <BODY bgcolor=\"lightgray\">\n <h1 align=\"center\">\n <font face=\"ºÚÌå\">\n <b>Preprocess Report</b>\n </font>\n </h1>
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37 <h2>1. Sequence No. and quality</h2>
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38 <h3>1.1 Sequece No.</h3>
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39 ";
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40
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41 ### raw data no
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42 open IN,"<$config";
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43 my @files;my @marks; my @rawNo;
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44 while (my $aline=<IN>) {
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45 chomp $aline;
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46 my @tmp=split/\t/,$aline;
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47 push @files,$tmp[0];
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48
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49 my $no=`less $tmp[0] |wc -l `;
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50 chomp $no;
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51 if ($opts{'format'} eq "fq" || $opts{'format'} eq "fastq") {
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52 $no=$no/4;
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53 }
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54 else{
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55 $no=$no/2;
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56 }
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57 push @rawNo,$no;
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58
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59 push @marks,$tmp[1];
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60 }
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61 close IN;
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62
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63 ### preprocess
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64 unless ($prepath=~/\/$/) {
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65 $prepath .="/";
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66 }
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67
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68 my @trimNo;my @collapse;
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69 my $collapsefile=$prepath."collapse_reads.fa";
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70 open IN,"<$collapsefile";
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71 while (my $aline=<IN>) {
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72 chomp $aline;
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73 <IN>;
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74 $aline=~/:([\d|_]+)_x(\d+)$/;
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75 my @lng=split/_/,$1;
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76 for (my $i=0;$i<@lng;$i++) {
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77 if ($lng[$i]>0) {
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78 $trimNo[$i] +=$lng[$i];
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79 $collapse[$i] ++;
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80 }
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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 my @cleanR;my @cleanT;
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86 my $clean=$prepath."collapse_reads_$opts{min}_$opts{max}.fa";
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87 open IN,"<$clean";
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88 while (my $aline=<IN>) {
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89 chomp $aline;
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90 <IN>;
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91 $aline=~/:([\d|_]+)_x(\d+)$/;
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92 my @lng=split/_/,$1;
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93 for (my $i=0;$i<@lng;$i++) {
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94 if ($lng[$i]>0) {
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95 $cleanR[$i] +=$lng[$i];
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96 $cleanT[$i] ++;
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97 }
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98 }
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99 }
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100 close IN;
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101
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102 print OUT "<table border=\"1\">
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103 <tr align=\"center\">
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104 <th> </th>
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105 ";
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106 foreach (@marks) {
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107 print OUT "<th> $_ </th>\n";
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108 }
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109 print OUT "</tr>
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110 <tr align=\"center\">
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111 <th align=\"left\">Raw Reads No. </th>
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112 ";
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113 foreach (@rawNo) {
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114 print OUT "<td> $_ </td>\n";
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115 }
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116 print OUT "</tr>
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117 <tr align=\"center\">
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118 <th align=\"left\">Reads No. After Trimed 3\' adapter </th>
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119 ";
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120 foreach (@trimNo) {
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121 print OUT "<td> $_ </td>\n";
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122 }
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123 print OUT "</tr>
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124 <tr align=\"center\">
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125 <th align=\"left\">Unique Tags No. </th>
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126 ";
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127 foreach (@collapse) {
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128 print OUT "<td> $_ </td>\n";
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129 }
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130 print OUT "</tr>
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131 <tr align=\"center\">
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132 <th align=\"left\">Clean Reads No. </th>
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133 ";
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134 foreach (@cleanR) {
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135 print OUT "<td> $_ </td>\n";
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136 }
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137 print OUT "</tr>
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138 <tr align=\"center\">
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139 <th align=\"left\">Clean Tags No. </th>
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140 ";
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141 foreach (@cleanT) {
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142 print OUT "<td> $_ </td>\n";
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143 }
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144 print OUT "</tr>\n</table>";
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145 print OUT "<p>
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146 Note:<br />
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147 The raw data file path is: <b>$files[0]</b><br />
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148 ";
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149 for (my $i=1;$i<@files;$i++) {
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150 print OUT "          <b>$files[$i]</b><br />";
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151 }
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152 print OUT "The collapsed file path is: <b>$collapsefile</b><br />
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153 The clean data file path is: <b>$clean</b><br />
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154 </p>
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155 <h2> 1. Sequence length count</h2>
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156 <h3> 1.1 Reads length count </h3>
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157 ";
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158 print OUT "\n";
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159
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160 my (%length); my $key="Tags Length";
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161 open IN,"<$prepath/reads_length_distribution.txt";
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162 while (my $aline=<IN>) {
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163 chomp $aline;
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164 next if($aline=~/^\s*$/);
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165 if ($aline=~/^Reads/) { $key="Reads Length";}
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166 my @tmp=split/\t/,$aline;
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167 my @array=split/\s/,$tmp[1];
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168 push @{$length{$key}},[$tmp[0],@array];
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169 }
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170 close IN;
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171
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172 print OUT "<table border=\"1\">
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173 <tr align=\"center\">";
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174 my $hashkey="Reads Length";
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175 foreach (@{$length{$hashkey}[0]}) {
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176 print OUT "<th> $_ </th>\n";
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177 }
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178 print OUT "</tr>";
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179
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180 for (my $i=1;$i<@{$length{$hashkey}};$i++) {
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181 print OUT "<tr align=\"center\">
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182 <th >$length{$hashkey}[$i][0] </th>
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183 ";
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184 for(my $j=1;$j<@{$length{$hashkey}[$i]};$j++) {
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185 print OUT "<td> $length{$hashkey}[$i][$j] </td>\n";
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186 }
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187 print OUT "</tr>\n";
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188 }
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189 print OUT "</table>\n";
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190
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191 print OUT "<h3> 1.2 Tags length count </h3>";
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192
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193 print OUT "<table border=\"1\">
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194 <tr align=\"center\">";
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195 $hashkey="Tags Length";
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196 foreach (@{$length{$hashkey}[0]}) {
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197 print OUT "<th> $_ </th>\n";
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198 }
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199 print OUT "</tr>";
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200
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201 for (my $i=1;$i<@{$length{$hashkey}};$i++) {
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202 print OUT "<tr align=\"center\">
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203 <th > $length{$hashkey}[$i][0] </th>
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204 ";
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205 for(my $j=1;$j<@{$length{$hashkey}[$i]};$j++) {
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206 print OUT "<td> $length{$hashkey}[$i][$j] </td>\n";
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207 }
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208 print OUT "</tr>\n";
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209 }
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210
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211 print OUT "</table>\n";
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212
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213 print OUT "<h2> 2. Sequence length distribution </h2>";
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214 my $length=$prepath."length.html";
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215 open IN,"<$length";
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216 while (my $aline=<IN>) {
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217 chomp $aline;
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218 print OUT "$aline\n";
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219 }
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220
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221 #print OUT "<p> Note:<br />The sequence length data: <a href=\"./$predir/reads_length_distribution.txt\"> length file</a>
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222 #</p>
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223 #";
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224
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225
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226
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227
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228 ####genome map
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229 #unless ($genomedir=~/\/$/) {
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230 # $genomedir .="/";
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231 #}
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232
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233 print OUT "<h2>2. Genome Alignment Result</h2>
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234 <h3>2.1 Mapping count</h3>
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235 ";
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236
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237 open IN,"<$genomepath/genome_mapped.fa";
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238 my (@gread,@gtag);
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239 while (my $aline=<IN>) {
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240 chomp $aline;
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241 <IN>;
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242 $aline=~/:([\d|_]+)_x(\d+)$/;
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243 my @sss=split/_/,$1;
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244 for (my $i=0;$i<@sss;$i++) {
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245 if ($sss[$i]>0) {
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246 $gread[$i] +=$sss[$i];
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247 $gtag[$i] ++;
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248 }
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249 }
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250 }
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251 close IN;
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252
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253 print OUT "<table border=\"1\">
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254 <tr align=\"center\">
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255 <th> </th>
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256 ";
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257 foreach (@marks) {
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258 print OUT "<th> $_ </th>\n";
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259 }
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260 print OUT "</tr>
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261 <tr align=\"center\">
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262 <th align=\"left\">Genome Mapped Reads No. </th>
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263 ";
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264 foreach (@gread) {
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265 print OUT "<td> $_ </td>\n";
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266 }
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267 print OUT "</tr>
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268 <tr align=\"center\">
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269 <th align=\"left\">Genome Mapped Reads Percent </th>
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270 ";
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271
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272 for (my $i=0;$i<@gread;$i++) {
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273 my $per=sprintf ("%.2f",$gread[$i]/$cleanR[$i]*100);
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274 print OUT "<td> $per\%</td>\n";
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275 }
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276
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277 print OUT "</tr>
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278 <tr align=\"center\">
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279 <th align=\"left\">Genome Mapped Tags No. </th>
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280 ";
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281 foreach (@gtag) {
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282 print OUT "<td> $_ </td>\n";
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283 }
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284 print OUT "</tr>
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285 <tr align=\"center\">
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286 <th align=\"left\">Genome Mapped Tags Percent </th>
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287 ";
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288
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289 for (my $i=0;$i<@gtag;$i++) {
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290 my $per=sprintf ("%.2f",$gtag[$i]/$cleanT[$i]*100);
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291 print OUT "<td> $per\%</td>\n";
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292 }
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293 print OUT "</tr>\n</table>";
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294 print OUT "<p>
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295 Note:<br />
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296 The genome mapped bwt file path is: <b>$genomedir/genome_mapped.bwt</b><br />
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297 The genome mapped FASTA file path is: <b>$genomedir/genome_mapped.fa</b>
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298 <br />
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299 ";
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300
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301
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302
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303 #### rfam
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304 if(defined $rfampath && $rfampath=~/rfam_match/){
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305 chomp $rfampath;
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306 @tmp=split/\//,$rfampath;
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307 $rfamdir=$tmp[-1];
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308
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309 unless ($rfampath=~/\/$/) {
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310 $rfampath .="/";
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311 }
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312 print OUT "<h2>3. Rfam non-miRNA annotation</h2>
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313 <h3>3.1 Reads count</h3>
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314 <table border=\"1\">
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315 <tr align=\"center\">
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316 ";
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317
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318 my @rfamR; my @rfamT;
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319 my $tag=1;
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320 open IN,"<$dir/rfam_non-miRNA_annotation.txt";
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321 while (my $aline=<IN>) {
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322 chomp $aline;
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323 $tag=0 if($aline=~/tags\s+number/);
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324 next if($aline=~/^\#/);
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325 next if($aline=~/^\s*$/);
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326 my @tmp=split/\s+/,$aline;
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327 if($tag == 1){push @rfamR,[@tmp];}
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328 else{push @rfamT,[@tmp];}
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329 }
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330 close IN;
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331
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332
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333 print OUT "<th>RNA Name</th>\n";
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334 foreach (@marks) {
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335 print OUT "<th> $_ </th>\n";
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336 }
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337 for (my $i=0;$i<@rfamR;$i++) {
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338 print OUT "</tr>
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339 <tr align=\"center\">
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340 <th align=\"left\">$rfamR[$i][0]</th>
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341 ";
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342 for (my $j=1;$j<@{$rfamR[$i]} ;$j++) {
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343 print OUT "<td> $rfamR[$i][$j]</td>\n";
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344 }
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345 }
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346
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347 print OUT "</tr>\n</table>
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348 <h3>3.2 Tags count</h3>
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349 <table border=\"1\">
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350 <tr align=\"center\">
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351 <th>RNA Name</th>\n";
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352 foreach (@marks) {
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353 print OUT "<th> $_ </th>\n";
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354 }
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355 for (my $i=0;$i<@rfamT;$i++) {
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356 print OUT "</tr>
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357 <tr align=\"center\">
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358 <th align=\"left\">$rfamT[$i][0]</th>
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359 ";
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360 for (my $j=1;$j<@{$rfamT[$i]} ;$j++) {
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361 print OUT "<td> $rfamT[$i][$j]</td>\n";
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362 }
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363 }
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364 print OUT "</tr>\n</table>
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365 <p>Note:<br />The rfam mapping results is: <b>$rfampath</b>";
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366 print OUT "<b>rfam_mapped.bwt</b></p>
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367 ";
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368 }
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369
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370
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371 print OUT "
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372 </BODY>
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373 </HTML>
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374 ";
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375 close OUT;
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376
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377 sub usage{
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378 print <<"USAGE";
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379 Version $version
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380 Usage:
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381 $0 -o
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382 options:
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383 -o output file
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384 -h help
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385 USAGE
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386 exit(1);
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387 }
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388
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