Perl script for extracting data - perl

Question

I have a file like this as shown below.
chr10 299448 299468 SRR048973.1457734 255 + 3
chr10 299448 299468 SRR048973.2114188 255 + 3
chr10 299448 299468 SRR048973.4148128 255 + 3
chr10 299945 299971 SRR048973.566192 255 + 6
chr10 299959 299982 SRR048973.762883 255 + 6
chr10 299968 299985 SRR048973.1595367 255 + 6
chr10 299968 299985 SRR048973.2828877 255 + 6
chr10 299968 299985 SRR048973.3711952 255 + 6
chr10 299968 299985 SRR048973.3821978 255 + 6
chr10 300073 300095 SRR048973.975870 255 + 1
chr10 300109 300134 SRR048973.1500469 255 + 1
chr10 300185 300209 SRR048973.655183 255 + 8
chr10 300185 300209 SRR048973.933425 255 + 8
chr10 300185 300209 SRR048973.963046 255 + 8
chr10 300185 300209 SRR048973.3506573 255 + 8
chr10 300185 300209 SRR048973.3627590 255 + 8
chr10 300186 300209 SRR048973.1133369 255 + 8
chr10 300186 300209 SRR048973.2178421 255 + 8
chr10 300186 300209 SRR048973.4047933 255 + 8
chr10 300401 300426 SRR048973.918503 255 + 2
chr10 300401 300426 SRR048973.2870188 255 + 2
Looking at the last column, if the last column is >= 5 then I want to count the lines till the column is greater than 5 until it falls back to < 5. Also the output I want should be like this for sample file
chr10 299945 299985 6
chr10 300185 300209 8
299945 comes from the 2nd column where the first 6 starts and 299985 comes from 3rd column where the last 6 ends. Similarly for 8.
I want to do this in Perl.
I tried writing the Perl script but cannot understand how to get coordinates properly.
#!/usr/bin/perl-w
use strict;
use warnings;
open F,'/user/tmp/output.bed',or die $!;
my $i=0;
while(<F>){
chomp;
my #s = split;
if($s[6] >= 5){
$i++;
}else{
if($s[6] < 5){
$i = 0;
}
}
}
How can I do it.
Thanks in advance
Regards

Answer 1

Use a range operator:
use strict;
use warnings;
my #last;
while (<DATA>) {
my #cols = split ' ';
if (my $range = $cols[-1] >= 5 .. $cols[-1] < 5 || eof) {
#last = #cols[0..2,-1] if $range == 1;
print "#last\n" if $range =~ /E/;
$last[2] = $cols[2];
}
}
__DATA__
chr10 299448 299468 SRR048973.1457734 255 + 3
chr10 299448 299468 SRR048973.2114188 255 + 3
chr10 299448 299468 SRR048973.4148128 255 + 3
chr10 299945 299971 SRR048973.566192 255 + 6
chr10 299959 299982 SRR048973.762883 255 + 6
chr10 299968 299985 SRR048973.1595367 255 + 6
chr10 299968 299985 SRR048973.2828877 255 + 6
chr10 299968 299985 SRR048973.3711952 255 + 6
chr10 299968 299985 SRR048973.3821978 255 + 6
chr10 300073 300095 SRR048973.975870 255 + 1
chr10 300109 300134 SRR048973.1500469 255 + 1
chr10 300185 300209 SRR048973.655183 255 + 8
chr10 300185 300209 SRR048973.933425 255 + 8
chr10 300185 300209 SRR048973.963046 255 + 8
chr10 300185 300209 SRR048973.3506573 255 + 8
chr10 300185 300209 SRR048973.3627590 255 + 8
chr10 300186 300209 SRR048973.1133369 255 + 8
chr10 300186 300209 SRR048973.2178421 255 + 8
chr10 300186 300209 SRR048973.4047933 255 + 8
chr10 300401 300426 SRR048973.918503 255 + 2
chr10 300401 300426 SRR048973.2870188 255 + 2
Outputs:
chr10 299945 299985 6
chr10 300185 300209 8

Answer 2

Do you need that counting? Your output seems to not incorporate it...
Using your code sample:
#!/usr/bin/perl-w
use strict;
use warnings;
open F,'/user/tmp/output.bed',or die $!;
my $i=0;
my $wasTheLastGreaterThan5 = 0;
while(<F>){
chomp;
my #s = split;
if(($s[6] >= 5) && !$wasTheLastGreaterThan5){
# Switched from smaller to greater than 5, do something here.
$wasTheLastGreaterThan5 = 1;
}elsif(($s[6] < 5) && $wasTheLastGreaterThan5){
# switched from greater to smaller, do something here.
$wasTheLastGreaterThan5 = 0;
}
else {
# Did not switch, if you need to count, you could do so here.
}
}