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Top Forums Shell Programming and Scripting Perl to adjust coordinates based on repeat string Post 303021900 by cmccabe on Monday 20th of August 2018 09:33:33 AM
Old 08-20-2018
Thank you @Aia, your perl is much more complete than mine. Can the header be included with each sequence and if there is no repeat in that sequence Nothing Detected results? Thank you very much Smilie.

Code:
>hg19_ncbiRefSeq_Gene range=chr2:166911123-166911301 5'pad=25 3'pad=25 strand=- repeatMasking=none
tttt range=chr2:166911127-166911130
tttt range=chr2:166911142-166911145
TTTT range=chr2:166911173-166911176
TTTT range=chr2:166911221-166911224
tttt range=chr2:166911287-166911290
>hg19_ncbiRefSeq_Gene range=chr2:166909337-166909478 5'pad=25 3'pad=25 strand=- repeatMasking=none
Nothing Detected

 

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Number::Range(3pm)					User Contributed Perl Documentation					Number::Range(3pm)

NAME
Number::Range - Perl extension defining ranges of numbers and testing if a number is found in the range. You can also add and delete from this range. SYNOPSIS
use Number::Range; my $range = Number::Range->new("-10..10,12,100..120"); if ($range->inrange("13")) { print "In range "; } else { print "Not in range "; } $range->addrange("200..300"); $range->delrange("250..255"); my $format = $range->range; # $format will be '-10..10,12,100..120,200..249,256..300' DESCRIPTION
Number::Range will take a description of a range, and then allow you to test on if a number falls within the range. You can also add and delete from the range. RANGE FORMAT The format used for range is pretty straight forward. To separate sections of ranges it uses a "," or whitespace. To create the range, it uses ".." to do this, much like Perl's own binary ".." range operator in list context. METHODS new $range = Number::Range->new("10..20","25..30"); Creates the range object. It will accept any number of ranges as its input. addrange $range->addrange("22"); This will also take any number of ranges as input and add them to the existing range. delrange $range->delrange("10"); This will also take any number of ranges as input and delete them from the existing range. inrange $range->inrange("26"); my @results = $range->inrange("27","200"); This will take one or more numbers and check if each of them exists in the range. If passed a list, and in array context, it will return a list of 0's or 1's, depending if that one was true or false in the list position. If in scalar context, it will return a single 1 if all are true, or a single 0 if one of them failed. range $format = $range->range; @numbers = $range->range; Depending on context this will return either an array of all the numbers found in the range, for list context. For scalar context it will return a range string. size $size = $range->size; This will return the total number of entries in the range. EXPORT None by default. SEE ALSO
Number::Tolerant, Tie::RangeHash, and Array::IntSpan for similar modules. AUTHOR
Larry Shatzer, Jr., <larrysh@cpan.org> COPYRIGHT AND LICENSE
Copyright (C) 2004-12 by Larry Shatzer, Jr. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. perl v5.14.2 2012-06-20 Number::Range(3pm)
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