プローブ間の間を示さないとだめじゃん。
#!/usr/bin/perl
#
# probedistance >>>>select_distance
$| = 1;
$infile = $ARGV[0];
$select_dist = $ARGV[1];
open(INFILE, "< $infile") || die "Can't open $infile";
while(<INFILE>) {
chomp;
push(@agiarray, $_);
push(@chr, (split(/\t/, $_))[1]);
push(@start, (split(/\t/, $_))[2]);
push(@end, (split(/\t/, $_))[3]);
push(@id, (split(/\t/, $_))[4]);
#print "$start $end $id\n";
}
foreach $i (0..$#end) {
if ($i !=0) {
$distance = $start[$i] - $end[$i-1];
$tempid = $id[$i];
print "$chr[$i]\t$end[$i-1]\t$start[$i]\t$tempid\_$id[$i-1]_$distance\n" if ($select_dist < $distance);
} else {
$distance = $start[$i] - 0;
print "$chr[0]\t0\t$start[0]\t$id[0]\_0_$distance\n" if ($select_dist < $distance);
}
}
~
~
~
[minako1@minako agilent]# grep "[[:space:]]chr10[[:space:]]" agilentCgh244a.txt | perl 20100301.pl - 100000
chr10 1994222 2160494 A_86_P04317089_A_86_P04316823_166272
chr10 3355287 3506329 A_86_P04320226_A_86_P04320204_151042
chr10 11258312 11411259 A_86_P04344161_A_86_P04344114_152947
chr10 17938351 18048353 A_86_P04364781_A_86_P04364780_110002
chr10 34307747 34631485 A_86_P04415780_A_86_P04415772_323738
chr10 35511521 35685071 A_86_P04418327_A_86_P04418324_173550
chr10 42755397 43072540 A_86_P04440080_A_86_P04440075_317143
chr10 50255526 50360126 A_86_P04462526_A_86_P04462516_104600
chr10 52041640 52166068 A_86_P04468130_A_86_P04468127_124428
chr10 52313041 52415013 A_86_P04468740_A_86_P04468456_101972
chr10 52704050 52839977 A_86_P04469787_A_86_P04469413_135927
chr10 66153902 66487506 A_86_P04510212_A_86_P04510179_333604
chr10 67926424 68268962 A_86_P04514853_A_86_P04514843_342538
chr10 74707366 74846046 A_86_P04536506_A_86_P04536505_138680
chr10 87949125 88104592 A_86_P04577507_A_86_P04577499_155467
chr10 93740007 93970524 A_86_P04595309_A_86_P04595293_230517
chr10 104286893 104487073 A_86_P04627551_A_86_P04627504_200180
[minako1@minako agilent]# grep "[[:space:]]chr10[[:space:]]" agilentCgh244a.txt | perl 20100301.pl - 100000 > chr10_100k_dist.v2.bed
[minako1@minako agilent]#
