annotate scripts/pickSoftClipping.over.pl @ 15:65ae84fc6689 draft

planemo upload for repository https://github.com/portiahollyoak/Tools commit 7e0a7a19ee51f12bdcdfe84f3de67530a8990de9
author portiahollyoak
date Mon, 23 May 2016 10:37:52 -0400
parents 28d1a6f8143f
children 9672fe07a232
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1 #!/share/bin/perl
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2 use Bio::Seq;
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3 use List::Util qw(sum);
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5 die "perl $0 <*.excision.cluster.rpmk> <Reference.2bit>\n" if @ARGV<1;
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7 my $title=$ARGV[0];
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8 if ($title =~ /annotation/) {
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9 $title =~ s/excision.cluster.annotation/sorted.bam/;
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10 }
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11 else {$title =~ s/excision.cluster.rpmk/sorted.bam/;}
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12
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13 my %chrs=();
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14 system("samtools view -H $title > header");
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15 open (input, "<header") or die "Can't open header since $!\n";
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16 while (my $line=<input>) {
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17 if ($line =~ /^\@SQ/) {
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18 my @a=split(/\t/, $line);
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19 for my $j (0..$#a) {
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20 if ($a[$j] =~ /^SN:/) {
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21 $a[$j] =~ s/^SN://;
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22 $chrs{$a[$j]}=1;
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23 }
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24 }
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25 }
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26 }
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27 close input;
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28 system("rm header");
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30 open (input, "<$ARGV[0]") or die "Can't open $ARGV[0] since $!\n";
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31 while (my $line=<input>) {
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32 chomp($line);
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33 my @a=split(/\s+/, $line);
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35 my $lower=$a[3]-100;
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36 my $upper=$a[4]+100;
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37 my $chr_num=$a[2];
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38 $chr_num =~ s/chr//;
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39 if (($chrs{$a[2]} == 1) && (! defined $chrs{$chr_num})) {$chr_num=$a[2];}
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40 system("samtools view -bu $title $chr_num\:$lower\-$upper > temp.bam");
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41 system("samtools view -Xf 0x2 temp.bam > temp.sam");
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42
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43 my $leftseq="";
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44 my $rightseq="";
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45
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46 my $ll=$a[3]-150;
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47 my $lu=$a[3]+150;
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48 system("twoBitToFa $ARGV[1] -seq=$a[2] -start=$ll -end=$lu left.fa");
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49 open (seq, "<left.fa") or die "Can't open left.fa since $!\n";
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50 my $head=<seq>;
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51 for my $k (0..5) {
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52 $head=<seq>;
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53 chomp($head);
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54 $leftseq=$leftseq."$head";
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55 }
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56 $leftseq=uc($leftseq);
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57 close seq;
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58 system("rm left.fa");
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59
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60 my $rl=$a[4]-150;
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61 my $ru=$a[4]+150;
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62 system("twoBitToFa $ARGV[1] -seq=$a[2] -start=$rl -end=$ru right.fa");
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63 open (seq, "<right.fa") or die "Can't open right.fa since $!\n";
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64 my $head=<seq>;
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65 for my $k (0..5) {
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66 $head=<seq>;
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67 chomp($head);
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68 $rightseq=$rightseq."$head";
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69 }
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70 $rightseq=uc($rightseq);
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71 close seq;
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72 system("rm right.fa");
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73
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74
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75 open in,"temp.sam";
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76 my %pe=();
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77 while(<in>)
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78 {
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79 chomp;
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80 my @f=split/\t/,$_,12;
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81 ## read number 1 or 2
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82 my ($rnum)=$f[1]=~/(\d)$/;
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83
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84 ## XT:A:*
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85 my ($xt)=$f[11]=~/XT:A:(.)/;
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86
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87 my $CIGAR=$f[5];
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88 $CIGAR =~ s/S//g;
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89 if ($f[5]=~/S/) {
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90
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91 ## Coordinate
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92 my $coor=-10;
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93 my $overcoor=-10;
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94 my $strand="";
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95 my @z=split(/M/, $f[5]);
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96
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97 if (($f[5]=~/S$/)&&($f[1]=~/r/))
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98 {
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99 my (@cigar_m)=$f[5]=~/(\d+)M/g;
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100 my (@cigar_d)=$f[5]=~/(\d+)D/g;
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101 my (@cigar_s)=$f[5]=~/(\d+)S/g;
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102 my (@cigar_i)=$f[5]=~/(\d+)I/g;
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103 my $aln_ln=sum(@cigar_m,@cigar_d);
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104 $coor=$f[3]+$aln_ln-1;
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105 $strand="-";
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106
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107 my (@clipped)=$z[1]=~/(\d+)S/g;
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108 my $cliplen=sum(@clipped);
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109 # print "$f[0]\n";
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110 # print "$cliplen\t";
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111 if ($cliplen >= 10) {
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112 my $clipseq=substr($f[9], length($f[9])-$cliplen, $cliplen);
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113 $overcoor = index($rightseq, $clipseq);
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114 # print "$clipseq\t$rightseq\t$overcoor\t";
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115 if ($overcoor > -1) {$overcoor += ($a[4] - 149);}
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116 }
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117 # print "\n";
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118 }
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119 elsif (($f[1]=~/R/)&&($z[0]=~/S/)) {
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120 $coor=$f[3]; $strand="+";
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121 my (@clipped)=$z[0]=~/(\d+)S/g;
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122 my $cliplen=sum(@clipped);
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123 # print "$f[0]\n";
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124 # print "$cliplen\t";
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125 if ($cliplen >= 10) {
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126 my $clipseq=substr($f[9], 0, $cliplen);
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127 $overcoor = index($leftseq, $clipseq);
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128 # print "$clipseq\t$leftseq\t$overcoor\t";
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129 if ($overcoor > -1) {$overcoor += ($a[3] - 150 + $cliplen);}
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130 }
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131 # print "\n";
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132 }
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133
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134 if ($coor > 0) {
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135 my $final="";
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136 if ($overcoor > 0) {
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137 if ($strand eq "-") {$final="$coor\-$overcoor"."\($strand\)";}
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138 else {$final="$overcoor\-$coor"."\($strand\)";}
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139 }
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140 else {$final=$coor."\($strand\)";}
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141 if (defined $pe{$final}) {$pe{$final}++;}
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142 else {$pe{$final}=1;}
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143 }
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144
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145 }
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146 }
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147 close in;
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148
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149 my $clip_site="";
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150
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151 foreach my $coor (keys %pe)
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152 {
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153 if ($pe{$coor} >= 2) {
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154 $clip_site=$clip_site."$coor\:$pe{$coor}\;";
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155 }
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156 }
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157
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158 chop($clip_site);
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159 print "$a[2]\t$a[3]\t$a[4]\t$a[5]\t$clip_site\n";
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160 system("rm temp.sam temp.bam");
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161 # last;
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162 }
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163