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Top Forums Shell Programming and Scripting Differential substring removal using coordinates Post 302584291 by vectorborne5 on Thursday 22nd of December 2011 04:20:27 PM
Old 12-22-2011
Works brilliantly!!! Thank you ahamed!

I made one slight adjustment so as to retain the unique id along with the core string:
Code:
awk 'NR==FNR{split($2,c,",");split($3,b,",");a[$1]=c[2]" "b[1]; next}{if($1 in a){split(a[$1],d," "); print $1 "\t" substr($2,d[1]+1,d[2]-d[1]-1)}}' coordinates.file tabular-fasta.file > ouput.file

 

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Perl::Critic::Policy::BuiltinFunctions::ProhibitStringySUser(Contributed Perl DocPerl::Critic::Policy::BuiltinFunctions::ProhibitStringySplit(3pm)

NAME
Perl::Critic::Policy::BuiltinFunctions::ProhibitStringySplit - Write "split /-/, $string" instead of "split '-', $string". AFFILIATION
This Policy is part of the core Perl::Critic distribution. DESCRIPTION
The "split" function always interprets the PATTERN argument as a regular expression, even if you specify it as a string. This causes much confusion if the string contains regex metacharacters. So for clarity, always express the PATTERN argument as a regex. $string = 'Fred|Barney'; @names = split '|', $string; #not ok, is ('F', 'r', 'e', 'd', '|', 'B', 'a' ...) @names = split m/[|]/, $string; #ok, is ('Fred', Barney') When the PATTERN is a single space the "split" function has special behavior, so Perl::Critic forgives that usage. See "perldoc -f split" for more information. CONFIGURATION
This Policy is not configurable except for the standard options. SEE ALSO
Perl::Critic::Policy::ControlStrucutres::RequireBlockGrep Perl::Critic::Policy::ControlStrucutres::RequireBlockMap AUTHOR
Jeffrey Ryan Thalhammer <jeff@imaginative-software.com> COPYRIGHT
Copyright (c) 2005-2011 Imaginative Software Systems. All rights reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself. The full text of this license can be found in the LICENSE file included with this module. perl v5.14.2 2012-06-07 Perl::Critic::Policy::BuiltinFunctions::ProhibitStringySplit(3pm)
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