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Top Forums UNIX for Dummies Questions & Answers Matching string and assembling Post 302969911 by RudiC on Wednesday 30th of March 2016 01:57:44 AM
Old 03-30-2016
T'was too late last night - sorry. Try
Code:
awk '
BEGIN           {for (i = split ("A C G T", Y); i>0; i--) R[Y[i]] = Y[5-i]
                }

function MM(CR) {for (i=0; i<length (CR); i++)  {X = substr (CR, 1, i) "." substr (CR, i+2)
                                                 for (j=i; j<length (CR); j++)  {T = substr (X,  1, j) "." substr (X,  j+2)
                                                                                 if (match (REF, T))  return 1
                                                                                }
                                                }
                 return 0
                }
/^>/            {SN = $0
                 next
                }
                {RV = ""
                 for (i = split ($0, A, ""); i>0; i--) RV = RV R[A[i]]
                 }
match (REF, $0) ||
MM($0)          {print SN ORS $0
                }
match (REF, RV) ||
MM(RV)          {print SN ORS RV
                }
' REF="AGAGAGACCTGGAGAGAGAGTGACGATGAGCAGTGACGATGACGTACGATAGCAGTAGACGCA" file
>read1 ori 498
AGAGAGACCTGGAGAGAGAGT
>read2 ori-rep 500
AGAGAGACCTGGAGAGAGAGT
>read3 1-misma 456
GGAGAGACCTGGAGAGAGAGT
>read4 2-misma 456
TGAGAGACCTGGAGAGAGAGA
>read5 ori-rev 532
AGAGAGACCTGGAGAGAGAGT
>read6 ori-rev-1-misma 499
GGAGAGACCTGGAGAGAGAGT
>read7 medium 512
AGAGAGAGTGACGATGAGCAG
>read8 last 488
AGTGACGATGACGTACGATAGCAGTAGACGCA
>read9 last rep 488
AGTGACGATGACGTACGATAGCAGTAGACGCA
>read10 last gap 488
AGTGACGATGACGTACGATAGCAGTAGACGA

This User Gave Thanks to RudiC For This Post:
 

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FindRef(3pm)						User Contributed Perl Documentation					      FindRef(3pm)

NAME
Devel::FindRef - where is that reference to my variable hiding? SYNOPSIS
use Devel::FindRef; print Devel::FindRef::track $some_variable; DESCRIPTION
Tracking down reference problems (e.g. you expect some object to be destroyed, but there are still references to it that keep it alive) can be very hard. Fortunately, perl keeps track of all its values, so tracking references "backwards" is usually possible. The "track" function can help track down some of those references back to the variables containing them. For example, for this fragment: package Test; use Devel::FindRef; use Scalar::Util; our $var = "hi "; my $global_my = $var; our %global_hash = (ukukey => $var); our $global_hashref = { ukukey2 => $var }; sub testsub { my $testsub_local = $global_hashref; print Devel::FindRef::track $var; } my $closure = sub { my $closure_var = $_[0]; Scalar::Util::weaken (my $weak_ref = $var); testsub; }; $closure->($var); The output is as follows (or similar to this, in case I forget to update the manpage after some changes): SCALAR(0x7cc888) [refcount 6] is +- referenced by REF(0x8abcc8) [refcount 1], which is | in the lexical '$closure_var' in CODE(0x8abc50) [refcount 4], which is | +- the closure created at tst:18. | +- referenced by REF(0x7d3c58) [refcount 1], which is | | in the lexical '$closure' in CODE(0x7ae530) [refcount 2], which is | | +- the containing scope for CODE(0x8ab430) [refcount 3], which is | | | in the global &Test::testsub. | | +- the main body of the program. | +- in the lexical '&' in CODE(0x7ae530) [refcount 2], which was seen before. +- referenced by REF(0x7cc7c8) [refcount 1], which is | in the lexical '$global_my' in CODE(0x7ae530) [refcount 2], which was seen before. +- in the global $Test::var. +- referenced by REF(0x7cc558) [refcount 1], which is | in the member 'ukukey2' of HASH(0x7ae140) [refcount 2], which is | +- referenced by REF(0x8abad0) [refcount 1], which is | | in the lexical '$testsub_local' in CODE(0x8ab430) [refcount 3], which was seen before. | +- referenced by REF(0x8ab4f0) [refcount 1], which is | in the global $Test::global_hashref. +- referenced by REF(0x7ae518) [refcount 1], which is | in the member 'ukukey' of HASH(0x7d3bb0) [refcount 1], which is | in the global %Test::global_hash. +- referenced by REF(0x7ae2f0) [refcount 1], which is a temporary on the stack. It is a bit convoluted to read, but basically it says that the value stored in $var is referenced by: - the lexical $closure_var(0x8abcc8), which is inside an instantiated closure, which in turn is used quite a bit. - the package-level lexical $global_my. - the global package variable named $Test::var. - the hash element "ukukey2", in the hash in the my variable $testsub_local in the sub "Test::testsub" and also in the hash "$referenced by Test::hash2". - the hash element with key "ukukey" in the hash stored in %Test::hash. - some anonymous mortalised reference on the stack (which is caused by calling "track" with the expression "$var", which creates the reference). And all these account for six reference counts. EXPORTS
None. FUNCTIONS
$string = Devel::FindRef::track $ref[, $depth] Track the perl value pointed to by $ref up to a depth of $depth and return a descriptive string. $ref can point at any perl value, be it anonymous sub, hash, array, scalar etc. This is the function you most often use. @references = Devel::FindRef::find $ref Return arrayrefs that contain [$message, $ref] pairs. The message describes what kind of reference was found and the $ref is the reference itself, which can be omitted if "find" decided to end the search. The returned references are all weak references. The "track" function uses this to find references to the value you are interested in and recurses on the returned references. $ref = Devel::FindRef::ptr2ref $integer Sometimes you know (from debugging output) the address of a perl scalar you are interested in (e.g. "HASH(0x176ff70)"). This function can be used to turn the address into a reference to that scalar. It is quite safe to call on valid addresses, but extremely dangerous to call on invalid ones. # we know that HASH(0x176ff70) exists, so turn it into a hashref: my $ref_to_hash = Devel::FindRef::ptr2ref 0x176ff70; $ref = Devel::FindRef::ref2ptr $reference The opposite of "ptr2ref", above: returns the internal address of the value pointed to by the passed reference. No checks whatsoever will be done, so don't use this. ENVIRONMENT VARIABLES
You can set the environment variable "PERL_DEVEL_FINDREF_DEPTH" to an integer to override the default depth in "track". If a call explicitly specified a depth it is not overridden. AUTHOR
Marc Lehmann <pcg@goof.com>. COPYRIGHT AND LICENSE
Copyright (C) 2007, 2008 by Marc Lehmann. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.8.8 or, at your option, any later version of Perl 5 you may have available. perl v5.14.2 2009-08-30 FindRef(3pm)
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