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Top Forums Shell Programming and Scripting Retrieving sequences corresponding to start and end position Post 303023753 by Ibk on Friday 21st of September 2018 03:45:18 PM
Old 09-21-2018
Retrieving sequences corresponding to start and end position

Hi all,

I have a fasta file of a reference sequnce, I will like to retrieve sequences corresponding to a list of start and end position in another file

Code:
>my_ref_seq
GCCCTATAAGGGCAGAAGCTTGTCCTTCTTGTGCCAGTTATGACGTTTGTCCTAACTGCACATCTGGTAG
CATCCCCGATGATGGGTCTTCCAAAGGACAGATCCCCTCCTGGGAAGATGTTACAAAAACTTCTACCTAC
TCTCTCTTGTTGTCTGAGGACACATCCGACGAACTGCACCCTGACGACCTGGTTAACGTTGCTGCTCATA
TCCGAAAGGCCTTGTCCACTCAGTCTCACCCGGCAAATGTTGATATGTGCAAAGAACAGCTCACATCTCT
GTTGGTTATGGCTGAAGCAATGCTACCCCAACGCTCTAGGTCGACACTCCCACTACACCAAAAATATGTG

position.txt
Code:
my_ref_seq    1550   1590    
my_ref_seq    2399   2429    
my_ref_seq    3008   3038

expected result
Code:
seq_id            Start   End     sequence
my_ref_seq    1550   1590    TCCGAAAGGCCTTGTCCACTCAGTCTCACC
my_ref_seq    2399   2429    TCTCTCTTGTTGTCTGAGGACACATCCGAC
my_ref_seq    3008   3038    GAACTGTCCGAAAGGCCTTGTCCACTCAAA

Thank you for the help.

Last edited by Scrutinizer; 09-21-2018 at 05:09 PM.. Reason: code tags
 

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Devel::Refcount(3pm)					User Contributed Perl Documentation				      Devel::Refcount(3pm)

NAME
"Devel::Refcount" - obtain the REFCNT value of a referent SYNOPSIS
use Devel::Refcount qw( refcount ); my $anon = []; print "Anon ARRAY $anon has " . refcount($anon) . " reference "; my $otherref = $anon; print "Anon ARRAY $anon now has " . refcount($anon) . " references "; DESCRIPTION
This module provides a single function which obtains the reference count of the object being pointed to by the passed reference value. FUNCTIONS
$count = refcount($ref) Returns the reference count of the object being pointed to by $ref. COMPARISON WITH SvREFCNT This function differs from "Devel::Peek::SvREFCNT" in that SvREFCNT() gives the reference count of the SV object itself that it is passed, whereas refcount() gives the count of the object being pointed to. This allows it to give the count of any referent (i.e. ARRAY, HASH, CODE, GLOB and Regexp types) as well. Consider the following example program: use Devel::Peek qw( SvREFCNT ); use Devel::Refcount qw( refcount ); sub printcount { my $name = shift; printf "%30s has SvREFCNT=%d, refcount=%d ", $name, SvREFCNT($_[0]), refcount($_[0]); } my $var = []; printcount 'Initially, $var', $var; my $othervar = $var; printcount 'Before CODE ref, $var', $var; printcount '$othervar', $othervar; my $code = sub { undef $var }; printcount 'After CODE ref, $var', $var; printcount '$othervar', $othervar; This produces the output Initially, $var has SvREFCNT=1, refcount=1 Before CODE ref, $var has SvREFCNT=1, refcount=2 $othervar has SvREFCNT=1, refcount=2 After CODE ref, $var has SvREFCNT=2, refcount=2 $othervar has SvREFCNT=1, refcount=2 Here, we see that SvREFCNT() counts the number of references to the SV object passed in as the scalar value - the $var or $othervar respectively, whereas refcount() counts the number of reference values that point to the referent object - the anonymous ARRAY in this case. Before the CODE reference is constructed, both $var and $othervar have SvREFCNT() of 1, as they exist only in the current lexical pad. The anonymous ARRAY has a refcount() of 2, because both $var and $othervar store a reference to it. After the CODE reference is constructed, the $var variable now has an SvREFCNT() of 2, because it also appears in the lexical pad for the new anonymous CODE block. PURE-PERL FALLBACK An XS implementation of this function is provided, and is used by default. If the XS library cannot be loaded, a fallback implementation in pure perl using the "B" module is used instead. This will behave identically, but is much slower. Rate pp xs pp 225985/s -- -66% xs 669570/s 196% -- SEE ALSO
o Test::Refcount - assert reference counts on objects AUTHOR
Paul Evans <leonerd@leonerd.org.uk> perl v5.14.2 2011-11-15 Devel::Refcount(3pm)
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