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Perl to adjust coordinates based on repeat string

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Top Forums Shell Programming and Scripting Perl to adjust coordinates based on repeat string
# 8  
Old 08-22-2018
Quote:
Originally Posted by cmccabe

In the line with > if the strand=+ then everything is good except that the calculated range=chr2:166170446-166170451 is 1 digit off. An example is

Code:
>hg19_ncbiRefSeq_SCN2A range=chr2:166168510-166168623 5'pad=25 3'pad=25 strand=+ repeatMasking=none
TTTTTT range=chr2:166168546-166168551

is

Code:
>hg19_ncbiRefSeq_SCN2A range=chr2:166168510-166168623 5'pad=25 3'pad=25 strand=+ repeatMasking=none
TTTTTT range=chr2:166168545-166168550

Does the sequence starts at 0 or does it start at 1?
Could you post the sequence that produces that result?

Quote:
Originally Posted by cmccabe
Code:
>hg19_ncbiRefSeq_SCN1A range=chr2:166905371-166905484 5'pad=25 3'pad=25 strand=- repeatMasking=none
catacgactttcttttttcaaacagGATATCATTATTTCCTGGAGGGTTT
TTTAGATGCACTACTATGTGGAAATAGCTCTGATGCAGGgtaagtcaata
atttgtgtgtatct

is

Code:
>hg19_ncbiRefSeq_SCN1A range=chr2:166905371-166905484 5'pad=25 3'pad=25 strand=- repeatMasking=none
AAAAAA chr2:166905432-166905437
aaaaaa chr2:166905467-166905472

[...]
I suppose I am not understanding. I cannot see how the above example AAAAAA or aaaaaa can be a match on the sequence catacgactttcttttttcaaacagGATATCATTATTTCCTGGAGGGTTT
TTTAGATGCACTACTATGTGGAAATAGCTCTGATGCAGGgtaagtcaata
atttgtgtgtatct
This User Gave Thanks to Aia For This Post:
cmccabe
# 9  
Old 08-22-2018
Quote:
Does the sequence starts at 0 or does it start at 1?
Could you post the sequence that produces that result?
1-based coordinate system where the t in green is 166168510 and the t in blue is 166168623. For a sequence that has strand=+ in the > line, the above will always be true and as you move to the right in the sequence the numbers increase from left to right as in the example below.

input
Code:
>hg19_ncbiRefSeq_SCN2A range=chr2:166168510-166168623 5'pad=25 3'pad=25 strand=+ repeatMasking=none
tttctattcctttctctttaaatagGTCACTTTTATTTTTTAGAGGGGCA
AAATGATGCTCTGCTTTGTGGCAACAGCTCAGATGCAGGgtaagtgatgc
ttcctactgagttt

current output
Code:
>hg19_ncbiRefSeq_SCN2A range=chr2:166168510-166168623 5'pad=25 3'pad=25 strand=+ repeatMasking=none
TTTTTT range=chr2:166168546-166168551

output with correct coordinates (the first T in the repeat is 35 away and there are 5 more repeat T in the sequence).
Code:
>hg19_ncbiRefSeq_SCN2A range=chr2:166168510-166168623 5'pad=25 3'pad=25 strand=+ repeatMasking=none
TTTTTT range=chr2:166168545-166168550

If in the line with > strand=-, then the last t in greenis 166905371 and the first c in blue is 166905484, the same 1-based coordinate system is applied, but the opposite orientation is true for strand=- and a compliment rule is applied and the numbers decrease from left to right as in the example.

input
Code:
>hg19_ncbiRefSeq_SCN1A range=chr2:166905371-166905484 5'pad=25 3'pad=25 strand=- repeatMasking=none
catacgactttcttttttcaaacagGATATCATTATTTCCTGGAGGGTTTTTTAGATGCACTACTATGTGGAAATAGCTCTGATGCAGGgtaagtcaata
atttgtgtgtatct

Compliment rules
Code:
Original repeat is A or a Compliment is T or t
Original repeat is T or t is Compliment is A or a
Original repeat is C or c is Compliment is G or g
Original repeat is G or g is Compliment is C or c

Since the first 6t in the repeat is at 166905472 and there are 5 more t after 166905467. The first coordinate (166905472), is the end, and the last coordinate (166905467) is the start. To further complicate things since the stand=- the 6t is really 6a following the Compliment rules.

Since the next 6T in the repeat is at 166905437 and there are 5 more t after 166905432. The first coordinate (166905437), is the end, and the last coordinate (166905432) is the start. To further complicate things since the stand=- the 6t is really 6A following the Compliment rules.


desired output
Code:
>hg19_ncbiRefSeq_SCN1A range=chr2:166905371-166905484 5'pad=25 3'pad=25 strand=- repeatMasking=none
AAAAAA chr2:166905432-166905437 --- these are the 6T in red
aaaaaa chr2:166905467-166905472  ---- the are the 6t in purple

The strand=- is a different process and unfortunately the rules that it uses only make it trickier.

I hope this helps and Thank you very much, I really appreciate all your help Smilie.
Last edited by cmccabe; 08-22-2018 at 11:15 AM.. Reason: added second question repose with example and description, added details
# 10  
Old 08-22-2018
Code:
cat example.fasta 
>hg19_ncbiRefSeq_Gene range=chr2:166911123-166911301 5'pad=25 3'pad=25 strand=- repeatMasking=none
aaattttttggatgcttgttttcagATACACCTTCACAGGAATATATACT
TTTGAATCACTTATAAAAATTATTGCAAGGGGATTCTGTTTAGAAGATTT
TACTTTCCTTCGGGATCCATGGAACTGGCTCGATTTCACTGTCATTACAT
TTGCgtaagtgccttttttgaaactttaa
>hg19_ncbiRefSeq_Gene range=chr2:166909337-166909478 5'pad=25 3'pad=25 strand=- repeatMasking=none
tttgtgtgtgaactccctattacagGTACGTCACAGAGTTTGTGGACCTG
GGCAATGTCTCGGCATTGAGAACATTCAGAGTTCTCCGAGCATTGAAGAC
>hg19_ncbiRefSeq_SCN2A range=chr2:166168510-166168623 5'pad=25 3'pad=25 strand=+ repeatMasking=none
tttctattcctttctctttaaatagGTCACTTTTATTTTTTAGAGGGGCA
AAATGATGCTCTGCTTTGTGGCAACAGCTCAGATGCAGGgtaagtgatgc
ttcctactgagttt
>hg19_ncbiRefSeq_SCN1A range=chr2:166905371-166905484 5'pad=25 3'pad=25 strand=- repeatMasking=none
catacgactttcttttttcaaacagGATATCATTATTTCCTGGAGGGTTTTTTAGATGCACTACTATGTGGAAATAGCTCTGATGCAGGgtaagtcaata
atttgtgtgtatct



Code:
#!/usr/bin/perl
use strict;
use warnings;

my @fasta = ();
my @m_results = ();
my @regexs;
my @rows = ('a', 't', 'c', 'g');
my @colums = (6 .. 25);

for my $r (@rows) {
    for my $c (@colums) {
        push @regexs, "$r\{$c\}";
    }
}

while(<>) {
    chomp;
    if(/^>/){
        if (@fasta) {
            @m_results = range_match(\@fasta);
            display();
        }
        @fasta = ();
        push @fasta, $_;
        next;
    }
    $fasta[1] .= $_;
}
@m_results = range_match(\@fasta);
display();

sub range_match {
    my $fref = shift;
    my @matches;
    my ($header, $seq) = @{$fref};
    my @hd_tokens = split /\s+/, $header;
    my ($mark, $beginning, $end) = split /[:-]/, $hd_tokens[1];

    if ($hd_tokens[4] =~ /=-/) {
        $seq =~ tr/[TtAaCcGg]/[AaTtGgCc]/;
        $seq = reverse $seq;
    }

    for my $regex (@regexs) {
        while($seq =~ /$regex/ig) {
            my $first = $-[0];
            my $last = $+[0] -1;
            push @matches, sprintf "%s %s:%s-%s\n", 
                $&, $mark, ($beginning + $first), ($beginning + $last);
        }
    }
    return @matches;
}

sub display {
    print "$fasta[0]\n";
    print @m_results ? @m_results : "Nothing Detected\n";
    @m_results = ();
}


Output:
Code:
 ./read_fasta.pl example.fasta
>hg19_ncbiRefSeq_Gene range=chr2:166911123-166911301 5'pad=25 3'pad=25 strand=- repeatMasking=none
aaaaaa range=chr2:166911133-166911138
aaaaaa range=chr2:166911293-166911298
>hg19_ncbiRefSeq_Gene range=chr2:166909337-166909478 5'pad=25 3'pad=25 strand=- repeatMasking=none
Nothing Detected
>hg19_ncbiRefSeq_SCN2A range=chr2:166168510-166168623 5'pad=25 3'pad=25 strand=+ repeatMasking=none
TTTTTT range=chr2:166168545-166168550
>hg19_ncbiRefSeq_SCN1A range=chr2:166905371-166905484 5'pad=25 3'pad=25 strand=- repeatMasking=none
AAAAAA range=chr2:166905432-166905437
aaaaaa range=chr2:166905467-166905472

This User Gave Thanks to Aia For This Post:
cmccabe
# 11  
Old 08-24-2018
Thank you very much, works great Smilie.
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