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94 lines
3.5 KiB
Perl
94 lines
3.5 KiB
Perl
#!/usr/bin/perl -w
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# This program detects overlapping indels in a chromosome and keeps all non-overlapping indels. As for overlapping indels,
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# the first encountered one is kept and all others are removed. It requires three inputs:
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# The first input is a TABULAR format file containing coordinates of indels in blocks extracted from multi-alignment.
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# The second input is an integer number representing the number of the column where indel start coordinates are stored in the input file.
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# The third input is an integer number representing the number of the column where indel end coordinates are stored in the input file.
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# The output is a TABULAR format file containing all non-overlapping indels in the input file, and the first encountered indel of overlapping ones.
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# Note: The number of the first column is 1.
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use strict;
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use warnings;
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#varaibles to handle information related to indels
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my $indel1 = "";
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my $indel2 = "";
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my @indelArray1 = ();
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my @indelArray2 = ();
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my $lineCounter1 = 0;
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my $lineCounter2 = 0;
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my $totalNumberofNonOverlappingIndels = 0;
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# check to make sure having correct files
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my $usage = "usage: delete_overlapping_indels.pl [TABULAR.in] [indelStartColumn] [indelEndColumn] [TABULAR.out]\n";
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die $usage unless @ARGV == 4;
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my $inputFile = $ARGV[0];
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my $indelStartColumn = $ARGV[1] - 1;
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my $indelEndColumn = $ARGV[2] - 1;
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my $outputFile = $ARGV[3];
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#verifie column numbers
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if ($indelStartColumn < 0 ){
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die ("The indel start column number is invalid \n");
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}
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if ($indelEndColumn < 0 ){
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die ("The indel end column number is invalid \n");
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}
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#open the input and output files
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open (INPUT, "<", $inputFile) || die ("Could not open file $inputFile \n");
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open (OUTPUT, ">", $outputFile) || die ("Could not open file $outputFile \n");
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#store the input file in the array @rawData
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my @indelsRawData = <INPUT>;
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#iterated through the indels of the input file
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INDEL1:
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foreach $indel1 (@indelsRawData){
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chomp ($indel1);
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$lineCounter1++;
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#get the first indel
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@indelArray1 = split(/\t/, $indel1);
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#our purpose is to detect overlapping indels and to store one copy of them only in the output file
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#all other non-overlapping indels will stored in the output file also
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$lineCounter2 = 0;
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#iterated through the indels of the input file
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INDEL2:
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foreach $indel2 (@indelsRawData){
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chomp ($indel2);
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$lineCounter2++;
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if ($lineCounter2 > $lineCounter1){
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#get the second indel
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@indelArray2 = split(/\t/, $indel2);
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#check if the two indels are overlapping
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if (($indelArray2[$indelEndColumn] >= $indelArray1[$indelStartColumn] && $indelArray2[$indelEndColumn] <= $indelArray1[$indelEndColumn]) || ($indelArray2[$indelStartColumn] >= $indelArray1[$indelStartColumn] && $indelArray2[$indelStartColumn] <= $indelArray1[$indelEndColumn])){
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#print ("There is an overlap between" . "\n" . $indel1 . "\n" . $indel2 . "\n");
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#print("The two overlapping indels are located at the lines: " . $lineCounter1 . " " . $lineCounter2 . "\n\n");
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#break out of the loop and go back to the outerloop
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next INDEL1;
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}
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else{
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#print("The two non-overlaapping indels are located at the lines: " . $lineCounter1 . " " . $lineCounter2 . "\n");
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}
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}
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}
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print OUTPUT $indel1 . "\n";
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$totalNumberofNonOverlappingIndels++;
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}
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#print("The total number of indels is: " . $lineCounter1 . "\n");
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#print("The total number of non-overlapping indels is: " . $totalNumberofNonOverlappingIndels . "\n");
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#close the input and output files
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close(OUTPUT);
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close(INPUT); |