Closed xie-wei-hh closed 1 year ago
oushujun
commented
2 years ago Hello @xie-wei-hh,
Sorry for the long delay. Thank you for helping to improve LTR_retriever! The code you provided is malformatted, can you please attach it as a separate file? You may use .txt instead of .pl to bypass the github requirement.
Best, Shujun
xie-wei-hh
commented
2 years ago Ok, I attached it here.
oushujun
commented
2 years ago Hello @xie-wei-hh,
Did you forget to attach the file? Thanks!
Shujun
xie-wei-hh
commented
2 years ago Hello, @oushujun Sorry, I didn't find the attach approach, so I wrongly attached it with e-mail. I find it now, as below: solo_intact_ratio.imroved.by.xw.txt
There may be a bug for the script solo_intact_ratio.pl. The intact LTR count always less 1 than the real count.
I fixed it like:
!/usr/bin/perl -w
use strict; use 5.010;
compute solo-intact LTR ratio for given lists
Shujun Ou (oushujun@msu.edu)
07-25-2017
update: 04/16/2019
my $usage="\n\tperl solo_intact_ratio.pl solo_list intact_list > solo_intact_ratio\n To make solo and intact lists: perl solo_finder.pl RepeatMasker.out > solo_list perl intact_finder_coarse.pl RepeatMasker.out > intact_list\n\n";
open Solo, "<$ARGV[0]" or die $usage; open Intact, "<$ARGV[1]" or die $usage;
my %intt; #intact my @ids=();
while (){
chomp;
s/^\s+//;
my $id=(split)[0];
$intt{$id}++; #count intact number
push @ids, $id unless ($id~~@ids)
}
close Intact;
my %solo; #solo while (){
chomp;
s/^\s+//;
my $id=(split)[0];
$solo{$id}++; #count solo number
if($id~~@ids){}else{push @ids, $id}
}
close Solo;
print "LTR_fam\tSolo_count\tIntact_count\tSolo-Intact-ratio\n"; my $ttlsolo=0; #total solo; my $ttlintt=0; #total intact; foreach my $id (sort {$a cmp $b} @ids){ my $ratio="NA"; if(!exists $solo{$id}){$solo{$id}=0;}; $intt{$id}=0 if (!exists $intt{$id}); my ($solo, $intact)=($solo{$id}, $intt{$id}); $ttlsolo += $solo; $ttlintt += $intact; if ($intact==0){ $ratio="NA"; #no intact LTR found for this family } elsif ($solo==0){ $ratio=0; } else { $ratio=sprintf ("%.2f", $solo/$intact); } print "$id\t$solo\t$intact\t$ratio\n"; } printf "summary\t$ttlsolo\t$ttlintt\t%.2f\n", $ttlsolo/$ttlintt;