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#!/usr/bin/perl -w
#>event_0_upper_path| A:183<206.22<239 B:104<154.08<182 |Cycle_0_upper_Length:101_coverage1:69_coverage2:63
#TTGATCCATAAATTGAGTCTGCAATAGTAAATGGAGCTTCAATATATTCATAAGCTTGAAGAATTGTAAAATAGATTCCTAGTAAAACTGTAAAAAATAAT
if(@ARGV !=3){
print "format:filter_coherenceNEW.pl coherent.txt events_tab_k.txt events_filtered.txt\n";
print "Please specify the names of the input files and the output file\n";
exit 1;
}
$infile1=shift; #idio me $infile=$ARGV[0]
#idio me $outfile= $ARGV[1]
$infile2=shift;
$outfile=shift;
open(IN1, "$infile1") || die "Cannot open: $!\n";
open(IN2, "$infile2") || die "Cannot open: $!\n";
open(OUT, ">$outfile") || die "Cannot open: $!\n";
while($line=<IN1>){
#>event_0_upper_path| A:183<206.22<239 B:104<154.08<182 |Cycle_0_upper_Length:101_coverage1:69_coverage2:63
#TTGATCCATAAATTGAGTCTGCAATAGTAAATGGAGCTTCAATATATTCATAAGCTTGAAGAATTGTAAAATAGATTCCTAGTAAAACTGTAAAAAATAAT
chomp($line);
if ($line=~m/>event(.*)\|(.*)\|Cycle_(\d+)_(.*)/){
$number=$3;
#print OUT1 "$number\n";
#print $number;
push(@coherent,$number);
}
}
@hash{@coherent}=();
while($line=<IN2>){
#Cycle Upperpath LowerPath Length_Upper Length_Lower Upper_Coverage_1 Upper_Coverage_2 Low_Coverage_1 Low_Coverage_2 Prediction
#0 TTGATCCATAAATTGAGTCTGCAATAGTAAATGGAGCTTCAATATATTCATAAGCTTGAAGAATTGTAAAATAGATTCCTAGTAAAACTGTAAAAAATAAT TTGATCCATAAATTGAGTCTGCAATAGTAAATGGAGCTTCAATATATTCACAAGCTTGAAGAATTGTAAAATAGATTCCTAGTAAAACTGTAAAAAATAAT 101 101 69 63 3 2
#2 GTTACTTTAGGGATAACAGCGTAATTTTTTTGGAGAGTTCATATCGATAAGAAAGATTGCGACCTCGATGTTGGATTAAGATATAATTTTGGGTGTAGCCG GTTACTTTAGGGATAACAGCGTAATTTTTTTGGAGAGTTCATATCGATAACAAAGATTGCGACCTCGATGTTGGATTAAGATATAATTTTGGGTGTAGCCG 101 101 56 34 57 33
chomp($line);
if ($line=~m/^Cycle(.*)/){
print OUT $line;
print OUT "\n";
}
if ($line=~m/^(\d+)\t(.*)/){
$number=$1;
print OUT "$line\n" if exists $hash{$number};
}
}
close(IN1);
close(IN2);
close(OUT);
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