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Full Discussion: Sequence extraction
Top Forums Shell Programming and Scripting Sequence extraction Post 302951305 by harpreetmanku04 on Wednesday 5th of August 2015 02:28:34 AM
Old 08-05-2015
Sequence extraction

i want to extract specific region of interest from big file. i have only start position, end position and seq id, see my query is:

I have file1 is this

Code:
>GL3482.1
GAACTTGAGATCCGGGGA
GCAGTGGATCTCCACCAG
CGGCCAGAACTGGTGCAC
CTCCAGGCCAGCCTCGTC
CTGCGTGTC
>GL3550.1
GGCATTTTTGTGTAATTTTTGGCTGGATGAGGT
GACATTTTCATTACTACCATTTTGGAGTACA
>GL3472.1
TTTTCCTGTTCACTGCTGCTTTTCTATAGACAGCA
GCAGCAAGCAGTAAGAGAAAGTA


file2 is this :

Code:
seq id     start    end
GL3482.1   323100   323743
GL3550.1   41911    40888
GL3472.1   274408   272617

and i want result like this:

Code:
>GL3482.1 
TTGAGA
>GL3550.1 
GGCATTTTTGTG
>GL3472.1
TTCCTGTT

when i run this command :

Code:
$ awk 'NR==FNR{if($0~/^>/){i=substr($0,2);getline};a[i]=a[i] $0;next}{print ">" $1 ORS substr(a[$1], $2, $3-$2+1)}' file1 FS=\\t file2

i got no output or output file. why so?
Moderator's Comments:
Mod Comment Please use CODE tags as required by the forum rules you agreed to when you joined this forum.


---------- Post updated at 01:28 AM ---------- Previous update was at 01:21 AM ----------

i am using Ubuntu OS

Last edited by Scrutinizer; 08-05-2015 at 04:07 AM.. Reason: Add CODE tags, remove extraneous closing COLOR tag. Removed spurious space and a newline from first sample file
 

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Locale::Codes::LangExt(3)				User Contributed Perl Documentation				 Locale::Codes::LangExt(3)

NAME
Locale::Codes::LangExt - standard codes for language extension identification SYNOPSIS
use Locale::Codes::LangExt; $lext = code2langext('acm'); # $lext gets 'Mesopotamian Arabic' $code = langext2code('Mesopotamian Arabic'); # $code gets 'acm' @codes = all_langext_codes(); @names = all_langext_names(); DESCRIPTION
The "Locale::Codes::LangExt" module provides access to standard codes used for identifying language extensions, such as those as defined in the IANA language registry. Most of the routines take an optional additional argument which specifies the code set to use. If not specified, the default IANA language registry codes will be used. SUPPORTED CODE SETS
There are several different code sets you can use for identifying language extensions. A code set may be specified using either a name, or a constant that is automatically exported by this module. For example, the two are equivalent: $lext = code2langext('acm','alpha'); $lext = code2langext('acm',LOCALE_LANGEXT_ALPHA); The codesets currently supported are: alpha This is the set of three-letter (lowercase) codes from the IANA language registry, such as 'acm' for Mesopotamian Arabic. This is the default code set. ROUTINES
code2langext ( CODE [,CODESET] ) langext2code ( NAME [,CODESET] ) langext_code2code ( CODE ,CODESET ,CODESET2 ) all_langext_codes ( [CODESET] ) all_langext_names ( [CODESET] ) Locale::Codes::LangExt::rename_langext ( CODE ,NEW_NAME [,CODESET] ) Locale::Codes::LangExt::add_langext ( CODE ,NAME [,CODESET] ) Locale::Codes::LangExt::delete_langext ( CODE [,CODESET] ) Locale::Codes::LangExt::add_langext_alias ( NAME ,NEW_NAME ) Locale::Codes::LangExt::delete_langext_alias ( NAME ) Locale::Codes::LangExt::rename_langext_code ( CODE ,NEW_CODE [,CODESET] ) Locale::Codes::LangExt::add_langext_code_alias ( CODE ,NEW_CODE [,CODESET] ) Locale::Codes::LangExt::delete_langext_code_alias ( CODE [,CODESET] ) These routines are all documented in the Locale::Codes::API man page. SEE ALSO
Locale::Codes The Locale-Codes distribution. Locale::Codes::API The list of functions supported by this module. http://www.iana.org/assignments/language-subtag-registry The IANA language subtag registry. AUTHOR
See Locale::Codes for full author history. Currently maintained by Sullivan Beck (sbeck@cpan.org). COPYRIGHT
Copyright (c) 2011-2013 Sullivan Beck This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. perl v5.16.3 2013-02-27 Locale::Codes::LangExt(3)
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