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1 use strict;
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2
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3 if(@ARGV == 0){
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4 die <<USAGE
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5 usage:
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6 perl extract_data.pl <chromFa> <bedfile> <chromcol> <startcol> <seccolm> <secondcol> <width> <statcol> <outfile>
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7
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8 <chromFa>: the chromosome FastA containing all chromosome sequences
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9 <bedfile>: the file containing the peaks in tabular format,
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10 e.g., bed, gff, narrowPeak
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11 <chromcol>: the column of <bedfile> containing the chromosome
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12 <startcol>: the column of <bedfile> containing the start position relative to
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13 the chromosome start
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14 <seccolm>: center: "Center of peak (relative to start)", end: "End of peak (global coordinates)"
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15 <secondcol>: the column of <bedfile> containing the peak center position (center) relative to
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16 <startcol> or the column of <bedfile> containing the end position (end)
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17 <width>: fixed width of all regions
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18 <statcol>: the column of <bedfile> containing the peak statistic
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19 or a similar measure of confidence
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20 <outfile>: the path to the output file, written as FastA
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21 USAGE
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22 }
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23
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24
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25 my $chromFa = $ARGV[0];
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26 my $bed = $ARGV[1];
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27 my $chromcol = $ARGV[2]-1;
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28 my $startcol = $ARGV[3]-1;
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29 my $seccolm = $ARGV[4];
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30 my $seccol = $ARGV[5]-1;
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31 my $width = $ARGV[6];
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32 my $statcol = $ARGV[7]-1;
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33 my $outfile = $ARGV[8];
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34
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35 my $sort = 1;
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36
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37
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38 sub loadSeq{
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39 my $prefix = shift;
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40 print $prefix," ";
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41 open(FA,$chromFa);
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42 my $head = "";
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43 my @lines = ();
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44 while(<FA>){
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45 chomp();
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46 if(/^>/){
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47 if($head){
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48 last;
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49 }
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50 if(/^>\s*(${prefix}|chr${prefix})(\s.*$|$)/i){
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51 $head = $_;
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52 }
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53 }elsif($head){
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54 push(@lines,lc($_));
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55 }
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56 }
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57 my $str = join("",@lines);
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58 print "loaded\n";
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59 return $str;
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60 }
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61
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62
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63
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64 open(IN,$ARGV[1]);
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65
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66 my @lines = ();
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67
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68 while(<IN>){
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69 chomp();
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70 my @parts = split("\t",$_);
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71 $parts[$chromcol] =~ s/chr0/chr/g;
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72 my @vals = ();
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73 if($seccolm eq "center"){
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74 @vals = ($parts[$chromcol],$parts[$startcol]+$parts[$seccol],$parts[$statcol]);
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75 }else{
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76 @vals = ($parts[$chromcol],int(($parts[$startcol]+$parts[$seccol])/2),$parts[$statcol]);
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77 }
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78 push(@vals,$width);
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79 push(@lines,\@vals);
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80 }
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81
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82 close(IN);
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83 #print "Read input file ".$bed."\n";
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84
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85
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86 if($sort){
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87
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88 @lines = sort { ${$a}[0] cmp ${$b}[0] } @lines;
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89
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90 }
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91
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92 open(OUT,">".$outfile);
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93
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94 print "Extracting sequences...\n\n";
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95
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96 my $oldchr = "";
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97 my $sequence = "";
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98 for my $line (@lines){
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99 my @ar = @{$line};
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100 my $chr = $ar[0];
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101 unless($chr eq $oldchr){
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102 $sequence = loadSeq($chr);
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103 }
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104 $oldchr = $chr;
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105 my $w = $ar[3];
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106 if($w <= 0){
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107 print $w," -> next\n";
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108 next;
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109 }
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110 if($w % 2 == 0){
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111 $w = $w/2;
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112 }else{
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113 $w = ($w-1)/2;
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114 }
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115
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116 my $start = $ar[1]-$w-1;
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117
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118 my $head = "> chr: ".$chr."; start: ".$start."; peak: ".($ar[1]-$start)."; signal: ".$ar[2]."\n";
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119 my $curr = substr($sequence,$start,$ar[3]);
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120 if($curr =~ /[^ACGTacgt]/){
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121 print "Sequence for\n\t",substr($head,1),"omitted due to ambiguous nucleotides.\n\n";
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122 }else{
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123 print OUT $head,$curr,"\n";
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124 }
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125 }
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126
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127 close(OUT);
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128 print "\nDone.\n"; |
