annotate scripts/pickClippedFastq.pl @ 16:c613f8c96e6d draft

planemo upload for repository https://github.com/portiahollyoak/Tools commit c734ef937d8ed788fded64ed8455e7fc7b89278c
author portiahollyoak
date Tue, 14 Jun 2016 04:36:25 -0400
parents 28d1a6f8143f
children 9672fe07a232
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 #!/share/bin/perl
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2 use List::Util qw(sum);
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3 use Bio::Seq;
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4
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5 die "perl $0 <input_prefix> <TE sequence database>\n" if @ARGV<1;
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6
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7 my %transposon_seq=();
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8 my %transposon_revcom_seq=();
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9 my $curr_seq="";
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10 my $curr_transposon="";
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11 open (input, "<$ARGV[1]") or die "Can't open $ARGV[1] since $!\n";
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12 while (my $line=<input>) {
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13 chomp($line);
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14 if ($line =~ /^\>/) {
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15 if ($curr_transposon ne "") {
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16 $transposon_seq{$curr_transposon}=uc($curr_seq);
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17 my $seq=Bio::Seq->new(-seq=>$curr_seq, -alphabet => 'dna');
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18 $curr_seq=$seq->revcom->seq;
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19 $transposon_revcom_seq{$curr_transposon}=uc($curr_seq);
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20 }
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21 my @a=split(/\s+/, $line);
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22 $a[0] =~ s/\>//;
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23 $curr_transposon=$a[0];
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24 $curr_seq="";
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25 }
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26 else {$curr_seq=$curr_seq.$line;}
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27 }
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28 close input;
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30 open m1,">>$ARGV[0].clipped.reads.aln";
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32 open (input, "<$ARGV[0].insertion.bp.bed") or die "Can't open $ARGV[0].insertion.bp.bed since $!\n";
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33 while (my $line=<input>) {
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34 chomp($line);
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35 my @a=split(/\t/, $line);
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36
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37 my $lower=$a[1]-15;
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38 my $upper=$a[2]+15;
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39 if (($lower > 0)&&($upper > 0))
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40 {
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41 system("samtools view -hXf 0x2 $ARGV[0].sorted.bam $a[0]\:$lower\-$upper > temp.sam");
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42
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43 open in,"temp.sam";
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44 my %pe1;
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45 my %pe2;
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46 while(<in>)
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47 {
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48 chomp;
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49 my @f=split/\t/,$_,12;
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50 ## read number 1 or 2
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51 my ($rnum)=$f[1]=~/(\d)$/;
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52
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53 ## XT:A:*
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54 my ($xt)=$f[11]=~/XT:A:(.)/;
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55
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56 if ($f[5]=~/S/) {
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57
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58 ## Coordinate
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59 my $coor=-10;
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60 my $strand="";
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61 my $final="";
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62 my $clipseq="";
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63 my @z=split(/M/, $f[5]);
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64
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65 if (($f[5]=~/S$/)&&($f[1]=~/r/))
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66 {
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67 my (@cigar_m)=$f[5]=~/(\d+)M/g;
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68 my (@cigar_d)=$f[5]=~/(\d+)D/g;
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69 my (@cigar_s)=$f[5]=~/(\d+)S/g;
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70 my (@cigar_i)=$f[5]=~/(\d+)I/g;
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71 my $aln_ln=sum(@cigar_m,@cigar_d);
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72 $coor=$f[3]+$aln_ln-1;
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73 $strand="-";
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74
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75 my (@clipped)=$z[1]=~/(\d+)S/g;
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76 my $cliplen=sum(@clipped);
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77 if ($cliplen >= 15) {
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78 $clipseq=substr($f[9], length($f[9])-$cliplen, $cliplen);
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79 }
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80 }
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81
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82 elsif (($f[1]=~/R/)&&($z[0]=~/S/))
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83 {
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84 $coor=$f[3]; $strand="+";
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85
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86 my (@clipped)=$z[0]=~/(\d+)S/g;
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87 my $cliplen=sum(@clipped);
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88 if ($cliplen >= 15) {
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89 $clipseq=substr($f[9], 0, $cliplen);
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90 }
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91 }
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92
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93 if ($clipseq ne "") {
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94 my $flag=0;
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95 while ((my $key, my $value) = each (%transposon_seq)) {
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96 my $seq=$value;
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97 if ($a[4] eq "antisense") {
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98 $seq=$transposon_revcom_seq{$key};
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99 }
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100 if (($seq =~ /$clipseq/)&&($a[3] eq $key)&&($coor >= $lower)&&($coor <= $upper)) {
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101 # print "$clipseq\n";
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102 $final=$coor."\($strand\)";
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103 if (defined $pe1{$final}) {
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104 if (length($clipseq) > length($pe1{$final})) {
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105 $pe1{$final}=$clipseq;
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106 }
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107 }
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108 else {$pe1{$final}=$clipseq; $pe2{$final}=0;}
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109 $flag=1;
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110 last;
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111 }
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112 }
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113 }
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114
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115 }
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116 }#while;
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117 close in;
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118
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119 open in,"temp.sam";
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120 while(<in>)
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121 {
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122 chomp;
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123 my @f=split/\t/,$_,12;
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124 my ($rnum)=$f[1]=~/(\d)$/;
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125 my ($xt)=$f[11]=~/XT:A:(.)/;
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126
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127 if ($f[5]=~/S/) {
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128
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129 my $coor=-10;
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130 my $strand="";
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131 my $final="";
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132 my $clipseq="";
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133 my @z=split(/M/, $f[5]);
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134
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135 if (($f[5]=~/S$/)&&($f[1]=~/r/))
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136 {
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137 my (@cigar_m)=$f[5]=~/(\d+)M/g;
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138 my (@cigar_d)=$f[5]=~/(\d+)D/g;
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139 my (@cigar_s)=$f[5]=~/(\d+)S/g;
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140 my (@cigar_i)=$f[5]=~/(\d+)I/g;
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141 my $aln_ln=sum(@cigar_m,@cigar_d);
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142 $coor=$f[3]+$aln_ln-1;
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143 $strand="-";
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144
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145 my (@clipped)=$z[1]=~/(\d+)S/g;
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146 my $cliplen=sum(@clipped);
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147 if ($cliplen >= 6) {
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148 $clipseq=substr($f[9], length($f[9])-$cliplen, $cliplen);
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149 }
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150 }
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151
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152 elsif (($f[1]=~/R/)&&($z[0]=~/S/))
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153 {
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154 $coor=$f[3]; $strand="+";
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155
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156 my (@clipped)=$z[0]=~/(\d+)S/g;
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157 my $cliplen=sum(@clipped);
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158 if ($cliplen >= 6) {
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159 $clipseq=substr($f[9], 0, $cliplen);
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160 }
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161 }
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162
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163 if ($clipseq ne "") {
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164 foreach my $coor (keys %pe1) {
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165 if (($coor =~ /\+/) && (substr($pe1{$coor}, length($pe1{$coor})-length($clipseq), length($clipseq)) eq $clipseq)) {
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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166 $pe2{$coor}++;
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167 }
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168 elsif (($coor =~ /\-/) && (substr($pe1{$coor}, 0, length($clipseq)) eq $clipseq)) {
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169 $pe2{$coor}++;
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170 }
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171 }
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172 }
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173 }
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174 }
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175 close in;
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176
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177 my $clip_site="";
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178
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179 foreach my $coor (keys %pe2)
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180 {
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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181 $clip_site=$clip_site."$coor\:$pe2{$coor}\;";
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182 }
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183 chop($clip_site);
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184 print m1 "$a[0]\t$lower\t$upper\t$a[3]\t$clip_site\n";
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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185 system("rm temp.sam");
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186 }
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187 else
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188 {
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189 print m1 "$line\n";
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190 }
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191 }
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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192 close input;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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193 close m1;