annotate miRPlant.pl @ 53:f5a2e8308836 draft default tip

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author big-tiandm
date Mon, 08 Dec 2014 01:51:16 -0500
parents 7b5a48b972e9
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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: 2014-4-22
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6 #Modified:
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7 #Description: plant microRNA prediction
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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 threads;
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13 #use threads::shared;
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14 use File::Path;
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15 use File::Basename;
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16 #use RNA;
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17 #use Term::ANSIColor;
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18
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19 my %opts;
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20 GetOptions(\%opts,"i:s@","tag:s@","phred:i","format=s","gfa=s","pre=s","mat=s","rfam:s","dis:i","flank:i","mfe:f","idx:s","idx2:s","mis:i","r:i","v:i","e:i","f:i","a:s","M:i","t:i","min:i","max:i","o:s","path:s","D","h");
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21 if (!(defined $opts{i} and defined $opts{format} and defined $opts{gfa} and defined $opts{pre} and defined $opts{mat}) || defined $opts{h}) { #necessary arguments
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22 &usage;
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23 }
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24
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25 my $time=&Time();
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26 print "miPlant program start:\n The time is $time!\n";
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27 print "Command line:\n $0 @ARGV\n";
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28
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29 my $format=$opts{'format'};
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30 if ($format ne "fastq" && $format ne "fq" && $format ne "fasta" && $format ne "fa") {
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31 #&printErr();
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32 die "Parameter \"-format\" is error! Parameter is fastq, fq, fasta or fa\n";
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33 }
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34
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35 my $phred_qv=64;
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36 if (defined $opts{'phred'}) {
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37 $phred_qv=$opts{'phred'};
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38 }
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39
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40 my @inputfiles=@{$opts{'i'}};
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41 my @inputtags=@{$opts{'tag'}};
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42
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43 my $mypath=`pwd`;
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44 chomp $mypath;
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45
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46 my $dir=defined $opts{'o'} ? $opts{'o'} : "$mypath/miRPlant_out/";
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47
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48
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49 unless ($dir=~/\/$/) {$dir.="/";}
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50 if (not -d $dir) {
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51 mkdir $dir;
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52 }
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53 my $config=$dir."/input_config";
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54 open CONFIG,">$config";
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55 for (my $i=0;$i<@inputfiles;$i++) {
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56 print CONFIG $inputfiles[$i],"\t",$inputtags[$i],"\n";
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57 }
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58 close CONFIG;
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59
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60 my $scipt_path=defined $opts{'path'} ? $opts{'path'} : "/Users/big/galaxy-dist/tools/myTools/";
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61
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62 my $a="ATCTCGTATG"; #adapter
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63 if (defined $opts{'a'}) {$a=$opts{'a'};}
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64
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65 my $m=6; #adapter minimum mapped nt
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66 if (defined $opts{'M'}) {$m=$opts{'M'};}
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67
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68 my $t=1; #threads number
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69 if (defined $opts{'t'}) {$t=$opts{'t'};}
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70
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71 my $min_nt=19; # minimum reads length
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72 if (defined $opts{'min'}) {$min_nt=$opts{'min'};}
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73
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74 my $max_nt=28; #maximum reads length
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75 if (defined $opts{'max'}) {$max_nt=$opts{'max'};}
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76
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77 my $mis=0; #mismatch number for microRNA
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78 if (defined $opts{'mis'}) {$mis=$opts{'mis'};}
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79
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80 my $mis_rfam=0;# mismatch number for rfam
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81 if (defined $opts{'v'}) {$mis_rfam=$opts{'v'};}
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82
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83 my $hit=25; # maximum reads mapping hits in genome
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84 if (defined $opts{'r'}) {$hit=$opts{'r'};}
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85
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86 my $upstream = 2; # microRNA 5' extension
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87 $upstream = $opts{'e'} if(defined $opts{'e'});
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88
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89 my $downstream = 5;# microRNA 3' extension
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90 $downstream = $opts{'f'} if(defined $opts{'f'});
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91
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92 my $maxd=defined $opts{'dis'} ? $opts{'dis'} : 200;
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93 my $flank=defined $opts{'flank'} ? $opts{'flank'} :10;
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94 my $mfe=defined $opts{'mfe'} ? $opts{'mfe'} : -20;
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95
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96 $time=&Time();
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97 print "$time, Checking input file!\n";
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98
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99 my (@filein,@mark,@clean);
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100 #&read_config();
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101 @filein=@inputfiles;
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102 @mark=@inputtags;
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103
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104 &checkfa($opts{pre});
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105 &checkfa($opts{mat});
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106 &checkfa($opts{gfa});
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107
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108
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109 ##### clip adpter --> clean data start
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110 $time=&Time();
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111 print "$time, Preprocess:\n trim adapter, reads collapse and filter reads by length.\n";
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112
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113 $time=~s/:/-/g;
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114 $time=~s/ /-/g;
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115 my $preprocess=$dir."preProcess_${time}/";
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116 mkdir $preprocess;
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117 my $can_use_threads = eval 'use threads; 1';
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118 if ($can_use_threads) {
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119 # Do processing using threads
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120 print "Do processing using threads\n";
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121 my @filein1=@filein; my @mark1=@mark;
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122 while (@filein1>0) {
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123 my @thrs; my @res;
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124 for (my $i=0;$i<$t ;$i++) {
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125 last if(@filein1==0);
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126 my $in=shift @filein1;
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127 my $out=shift @mark1;
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128 push @clean,$preprocess.$out."_clips_adapter.fq";
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129 $thrs[$i]=threads->create(\&clips,$in,$out);
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130 }
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131 for (my $i=0;$i<@thrs;$i++) {
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132 $res[$i]=$thrs[$i]->join();
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133 }
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134 }
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135 } else {
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136 # Do not processing using threads
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137 print "Do not processing using threads\n";
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138 for (my $i=0;$i<@filein ;$i++) {
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139 my $in=$filein[$i];
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140 my $out=$mark[$i];
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141 push @clean,$preprocess.$out."_clips_adapter.fq";
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142 &clips($in,$out);
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143 }
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144 }
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145
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146 ##### clip adpter --> clean data end
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147
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148 my $collapsed=$preprocess."collapse_reads.fa";
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149 my $data=$preprocess."collapse_reads_${min_nt}_${max_nt}.fa"; ## raw clean data
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150 my $data2; ### mirbase not mapped reads
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151 my $data3; ### rfam not mapped reads
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152 &collapse(\@clean,$collapsed); #collapse reads to tags
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153
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154 &filterbylength(); # filter <$min_nt && >$max_nt
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155
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156 print "The final clean data file is $data, only contains reads which length is among $min_nt\~$max_nt\n\n";
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157
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158 $time=Time();
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159 print "$time: known microRNA quantify!\n\n";
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160
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161 chdir $dir;
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162
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163 $time=~s/:/-/g;
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164 $time=~s/ /-/g;
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165 my $known_result=$dir."miRNA_Express_${time}/";
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166 &quantify(); ### known microRAN quantify
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167
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168
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169 #my $miR_exp_dir=&search($known_result,"miRNA_Express_");
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170 $data2=$known_result."/mirbase_not_mapped.fa";
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171
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172 my $pathfile="$dir/path.txt";
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173 open PA,">$pathfile";
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174 print PA "$config\n";
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175 print PA "$preprocess\n";
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176 print PA "$known_result\n";
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177
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178 if (defined $opts{'rfam'}) { #rfam mapping and analysis
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179 $time=Time();
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180 print "$time: RNA annotate!\n\n";
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181 $time=~s/:/-/g;
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182 $time=~s/ /-/g;
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183 my $rfam_exp_dir=$dir."rfam_match_${time}";
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184 &rfam();
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185 #my $rfam_exp_dir=&search($dir,"rfam_match_");
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186 $data3=$rfam_exp_dir."/rfam_not_mapped.fa";
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187 print PA "$rfam_exp_dir\n";
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188
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189 my $tag=join "\\;" ,@mark;
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190 system("perl $scipt_path/count_rfam_express.pl -i $rfam_exp_dir/rfam_mapped.bwt -tag $tag -o rfam_non-miRNA_annotation.txt");
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191 }
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192
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193 my $data4=$data;
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194 if (defined $opts{'D'}) { #genome mapping
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195 $data4=$data3;
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196 }else{
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197 $data4=$data2;
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big-tiandm
parents:
diff changeset
198 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
199
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
200 $time=Time();
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
201 print "$time: Genome alignment!\n\n";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
202 $time=~s/:/-/g;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
203 $time=~s/ /-/g;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
204 my $genome_map=$dir."genome_match_${time}";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
205 &genome($data4);
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
206 print PA "$genome_map\n";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
207 #my $genome_map=&search($dir,"genome_match_");
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
208 my $mapfile=$genome_map."/genome_mapped.bwt";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
209 my $mapfa=$genome_map."/genome_mapped.fa";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
210 my $unmap=$genome_map."/genome_not_mapped.fa";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
211
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
212 #$time=Time();
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
213 #print "$time: Novel microRNA prediction!\n\n";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
214
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
215 &predict($mapfa);
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
216
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
217 close PA;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
218 system("perl $scipt_path/html.pl -i $pathfile -format $format -o $dir/result.html");
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
219
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
220 $time=Time();
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
221 print "$time: Program end!!\n";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
222
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
223 ############################## sub programs ###################################
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
224 sub predict{
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
225 my ($file)=@_;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
226 $time=&Time();
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
227 print "$time: Novel microRNA prediction!\n\n";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
228 $time=~s/:/-/g;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
229 $time=~s/ /-/g;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
230 my $predict=$dir."miRNA_predict_${time}";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
231 print PA "$predict\n";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
232 mkdir $predict;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
233 chdir $predict;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
234 system("perl $scipt_path/precursors.pl -map $mapfile -g $opts{gfa} -d $maxd -f $flank -o $predict/excised_precursor.fa -s $predict/excised_precursor_struc.txt -e $mfe");
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
235 # print "\nprecursors.pl -map $mapfile -g $opts{gfa} -d $maxd -f $flank -o $predict/excised_precursor.fa -s $predict/excised_precursor_struc.txt -e $mfe\n";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
236
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
237 system("bowtie-build -f excised_precursor.fa excised_precursor");
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
238 # print "\nbowtie-build -f excised_precursor.fa excised_precursor\n";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
239
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
240 system("bowtie -v $mis -f -p $t -m $hit -a --best --strata excised_precursor $file > precursor_mapped.bwt 2> run.log");
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
241 # print "\nbowtie -v $mis -f -p $t -m $hit -a --best --strata excised_precursor $file > precursor_mapped.bwt\n";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
242
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
243 system("perl $scipt_path/convert_bowtie_to_blast.pl precursor_mapped.bwt $file excised_precursor.fa > precursor_mapped.bst");
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
244 # print "\nconvert_bowtie_to_blast.pl precursor_mapped.bwt $file excised_precursor.fa > precursor_mapped.bst\n";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
245
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
246 system("sort -k 4 precursor_mapped.bst > signatures.bst");
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
247 # print "\nsort +3 -25 precursor_mapped.bst > ../signatures.bst\n";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
248
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
249 chdir $dir;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
250 system("perl $scipt_path/miRDeep_plant.pl $predict/signatures.bst $predict/excised_precursor_struc.txt novel_tmp_dir -y > microRNA_prediction.mrd");
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
251 # print "\nmiRDeep_plant.pl $dir/signatures.bst $predict/excised_precursor_struc.txt tmp_dir -y > microRNA_prediction.txt\n";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
252 #system("rm novel_tmp_dir -rf");
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
253 my $tag=join "," ,@mark;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
254 system("perl $scipt_path/miRNA_Express_and_sequence.pl -i microRNA_prediction.mrd -list novel_microRNA_express.txt -fa novel_microRNA_mature.fa -pre novel_microRNA_precursor.fa -tag $tag");
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
255 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
256
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
257 sub genome{
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
258 my ($file)=@_;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
259 if(defined $opts{'idx'}){
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
260 system("perl $scipt_path/matching.pl -i $file -g $opts{gfa} -v $mis -p $t -r $hit -o $dir -index $opts{idx} -time $time") ;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
261 # print "\nmatching.pl -i $file -g $opts{gfa} -v $mis -p $t -r $hit -o $dir -index $opts{idx} -time $time\n";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
262 }else{
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
263 system("perl $scipt_path/matching.pl -i $file -g $opts{gfa} -v $mis -p $t -r $hit -o $dir -time $time") ;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
264 # print "\nmatching.pl -i $file -g $opts{gfa} -v $mis -p $t -r $hit -o $dir -time $time\n";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
265 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
266 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
267 sub rfam{
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
268 if (defined $opts{'idx2'}) {
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
269 system("perl $scipt_path/rfam.pl -i $data2 -ref $opts{rfam} -v $mis_rfam -p $t -o $dir -index $opts{idx2} -time $time");
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
270 # print "\nrfam.pl -i $data2 -ref $opts{rfam} -v $mis_rfam -p $t -o $dir -index $opts{idx2} -time $time\n";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
271 }else{
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
272 system("perl $scipt_path/rfam.pl -i $data2 -ref $opts{rfam} -v $mis_rfam -p $t -o $dir -time $time");
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
273 # print "\nrfam.pl -i $data2 -ref $opts{rfam} -v $mis_rfam -p $t -o $dir -time $time\n";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
274 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
275 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
276 sub quantify{
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
277 my $tag=join "\\;" ,@mark;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
278 system("perl $scipt_path/quantify.pl -p $opts{pre} -m $opts{mat} -r $data -o $dir -time $time -mis $mis -t $t -e $upstream -f $downstream -tag $tag");
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
279 print "\nquantify.pl -p $opts{pre} -m $opts{mat} -r $data -o $dir -time $time -mis $mis -t $t -e $upstream -f $downstream -tag $tag\n";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
280 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
281 sub filterbylength{
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
282 my $tmpmark=join ",", @mark;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
283 system("perl $scipt_path/filterReadsByLength.pl -i $collapsed -o $data -min $min_nt -max $max_nt -mark $tmpmark");
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
284 system("perl $scipt_path/Length_Distibution.pl -i $preprocess/reads_length_distribution.txt -o $preprocess/length.html");
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
285 # print "\nfilterReadsByLength.pl -i $collapsed -o $data -min $min_nt -max $max_nt -mark $tmpmark\n";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
286
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
287 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
288 sub collapse{
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
289 my ($ins,$data)=@_;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
290 my $str="";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
291 for (my $i=0;$i<@{$ins};$i++) {
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
292 $str .="-i $$ins[$i] ";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
293 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
294 system ("perl $scipt_path/collapseReads2Tags.pl $str -mark seq -o $data -format $format");
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
295 # print "\ncollapseReads2Tags.pl $str -mark seq -o $data -format $format\n";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
296 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
297
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
298 sub clips{
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
299 my ($in,$out)=@_;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
300 my $adapter=$preprocess.$out."_clips_adapter.fq";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
301 if($format eq "fq" || $format eq "fastq"){
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
302 system("fastx_clipper -a $a -M $m -Q $phred_qv -i $in -o $adapter") ;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
303 print "\nfastx_clipper -a $a -M $m -Q $phred_qv -i $in -o $adapter\n";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
304 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
305 if($format eq "fa" || $format eq "fasta"){
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
306 system("fastx_clipper -a $a -M $m -i $in -o $adapter") ;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
307 # print "\nfastx_clipper -a $a -M $m -i $in -o $adapter\n";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
308 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
309 #my $clean=$preprocess.$out."_clean.fq";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
310 #system("filterReadsByLength.pl -i $adapter -o $clean -min $min_nt -max $max_nt ");
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
311
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
312 return;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
313 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
314
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
315 sub read_config{
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
316 open CON,"<$config";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
317 while (my $aline=<CON>) {
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
318 chomp $aline;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
319 my @tmp=split/\t/,$aline;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
320 push @filein,$tmp[0];
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
321 push @mark,$tmp[1];
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
322 &check_rawdata($tmp[0]);
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
323 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
324 close CON;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
325 if (@filein != @mark) {
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
326 #&printErr();
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
327 die "Maybe config file have some wrong!!!\n";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
328 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
329 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
330 sub check_rawdata{
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
331 my ($fileforcheck)=@_;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
332 if (!(-s $fileforcheck)) {
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
333 #&printErr();
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
334 die "Can not find $fileforcheck, or file is empty!!!\n";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
335 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
336 if ($format eq "fasta" || $format eq "fa") {
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
337 &checkfa($fileforcheck);
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
338 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
339 if ($format eq "fastq" || $format eq "fq") {
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
340 &checkfq($fileforcheck);
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
341 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
342 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
343 sub checkfa{
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
344 my ($file_reads)=@_;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
345 open N,"<$file_reads";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
346 my $line=<N>;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
347 chomp $line;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
348 if($line !~ /^>\S+/){
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
349 #printErr();
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
350 die "The first line of file $file_reads does not start with '>identifier'
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
351 Reads file $file_reads is not a valid fasta file\n\n";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
352 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
353 if(<N> !~ /^[ACGTNacgtn]*$/){
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
354 #printErr();
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
355 die "File $file_reads contains not allowed characters in sequences
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
356 Allowed characters are ACGTN
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
357 Reads file $file_reads is not a fasta file\n\n";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
358 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
359 close N;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
360 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
361 sub checkfq{
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
362 my ($file_reads)=@_;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
363
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
364 open N,"<$file_reads";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
365 for (my $i=0;$i<10;$i++) {
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
366 my $a=<N>;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
367 my $b=<N>;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
368 my $c=<N>;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
369 my $d=<N>;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
370 chomp $a;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
371 chomp $b;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
372 chomp $c;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
373 chomp $d;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
374 if($a!~/^\@/){
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
375 #&printErr();
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
376 die "$file_reads is not a fastq file\n\n";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
377 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
378 if($b!~ /^[ACGTNacgtn]*$/){
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
379 #&printErr();
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
380 die "File $file_reads contains not allowed characters in sequences
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
381 Allowed characters are ACGTN
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
382 Reads file $file_reads is not a fasta file\n\n";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
383 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
384 if ($c!~/^\@/ && $c!~/^\+/) {
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
385 #&printErr();
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
386 die "$file_reads is not a fastq file\n\n";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
387 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
388 if ((length $b) != (length $d)) {
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
389 #&printErr();
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
390 die "$file_reads is not a fastq file\n\n";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
391 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
392 my @qv=split //,$d;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
393 for (my $j=0;$j<@qv ;$j++) {
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
394 my $q=ord($qv[$j])-64;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
395 if($q<0){$phred_qv=33;}
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
396 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
397 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
398 close N;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
399 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
400
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
401 sub search{
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
402 my ($dir,$str)=@_;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
403 opendir I,$dir;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
404 my @ret;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
405 while (my $file=readdir I) {
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
406 if ($file=~/$str/) {
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
407 push @ret, $file;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
408 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
409 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
410 closedir I;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
411 if (@ret != 1) {
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
412 #&printErr();
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
413
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
414 die "Can not find directory or file which name has string: $str !!!\n";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
415 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
416 return $ret[0];
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
417 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
418
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
419 =cut
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
420
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
421 sub printErr{
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
422 print STDERR color 'bold red';
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
423 print STDERR "Error: ";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
424 print STDERR color 'reset';
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
425 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
426 sub Time{
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
427 my $time=time();
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
428 my ($sec,$min,$hour,$day,$month,$year) = (localtime($time))[0,1,2,3,4,5,6];
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
429 $month++;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
430 $year+=1900;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
431 if (length($sec) == 1) {$sec = "0"."$sec";}
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
432 if (length($min) == 1) {$min = "0"."$min";}
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
433 if (length($hour) == 1) {$hour = "0"."$hour";}
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
434 if (length($day) == 1) {$day = "0"."$day";}
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
435 if (length($month) == 1) {$month = "0"."$month";}
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
436 #print "$year-$month-$day $hour:$min:$sec\n";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
437 return("$year-$month-$day-$hour-$min-$sec");
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
438 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
439 =cut
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
440 sub Time{
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
441 my $time=time();
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
442 my ($sec,$min,$hour,$day,$month,$year) = (localtime($time))[0,1,2,3,4,5,6];
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
443 $month++;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
444 $year+=1900;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
445 if (length($sec) == 1) {$sec = "0"."$sec";}
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
446 if (length($min) == 1) {$min = "0"."$min";}
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
447 if (length($hour) == 1) {$hour = "0"."$hour";}
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
448 if (length($day) == 1) {$day = "0"."$day";}
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
449 if (length($month) == 1) {$month = "0"."$month";}
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
450 #print "$year-$month-$day $hour:$min:$sec\n";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
451 return("$year-$month-$day $hour:$min:$sec");
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
452 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
453
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
454
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
455 sub usage{
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
456 print <<"USAGE";
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
457 Version $version
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
458 Usage:
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
459
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
460 $0 -i -format -gfa -index -pre -mat -rfam -D -a -M -min -max -mis -e -f -v -t -o -path
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
461 options:
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
462 -i input files, # raw data file, can be multipe eg. -i xxx.fq -i xxx .fq ...
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
463 -tag string # raw data file names, -tag xxx -tag xxx
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
464
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
465 -format string,#specific input rawdata file format : fastq|fq|fasta|fa
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
466
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
467 -path scirpt path
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
468
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
469 -gfa string, input file # genome fasta. sequence file
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
470 -idx string, genome file index, file-prefix #(must be indexed by bowtie-build) The parameter
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
471 string must be the prefix of the bowtie index. For instance, if
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
472 the first indexed file is called 'h_sapiens_37_asm.1.ebwt' then
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
473 the prefix is 'h_sapiens_37_asm'.##can be null
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
474
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
475 -pre string, input file #species specific microRNA precursor sequences
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
476 -mat string, input file #species specific microRNA mature sequences
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
477
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
478 -rfam string, input file# rfam database file, microRNAs must not be contained in this file## if not define, rfam small RNA will not be count.
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
479 -idx2 string, rfam file index, file-prefix #(must be indexed by bowtie-build) The parameter
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
480 string must be the prefix of the bowtie index. For instance, if
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
481 the first indexed file is called 'h_sapiens_37_asm.1.ebwt' then
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
482 the prefix is 'h_sapiens_37_asm'.##can be null
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
483
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
484 -D If [-D] is specified,will discard rfam mapped reads(nead -rfam).
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
485
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
486 -a string, ADAPTER string. default is ATCTCGTATG.
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
487 -M int, require minimum adapter alignment length of N. If less than N nucleotides aligned with the adapter - don't clip it.
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
488 -min int, reads min length,default is 19.
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
489 -max int, reads max length,default is 28.
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
490
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
491 -mis [int] number of allowed mismatches when mapping reads to precursors, default 0
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
492 -e [int] number of nucleotides upstream of the mature sequence to consider, default 2
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
493 -f [int] number of nucleotides downstream of the mature sequence to consider, default 5
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
494 -v <int> report end-to-end hits w/ <=v mismatches; ignore qualities,default 0; used in rfam alignment
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
495 -r int a read is allowed to map up to this number of positions in the genome,default is 25
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
496
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
497 -dis <int> Maximal space between miRNA and miRNA* (200)
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
498 -flank <int> Flank sequence length of miRNA precursor (10)
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
499 -mfe <folat> Maximal free energy allowed for a miRNA precursor (-20)
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
500
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
501 -t int, number of threads [1]
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
502
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
503 -o output directory# absolute path
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
504 -h help
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
505 USAGE
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
506 exit(1);
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
507 }
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
508