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Top Forums UNIX for Beginners Questions & Answers awk do not split if condition is meet Post 303036079 by cmccabe on Thursday 13th of June 2019 04:10:43 PM
Old 06-13-2019
awk do not split if condition is meet

Trying to use awk to format the input based on the filed count being 5. Most lines are fine using the awk below, except the first two lines. I know the reason is the -1 in green and -2 in blue. But can not figure out how to not split on the - if it is followed by a digit then letter. Thank you Smilie.

input

Code:
chr9:21971208 CDKN2A c.151-1G>A p.?
chr9:21971209 CDKN2A c.151-2A>G p.?
chr5:112175216 APC c.3925G>T p.E1309*
chr5:112175363 APC c.4072G>A p.A1358T
chr5:112175390 APC c.4099C>T p.Q1367*
EGFR,,EGFR c.2240_2257delTAAGAGAAGCAACATCTC p.L747_P753delinsS,chr7:55242470_55242487delTAAGAGAAGCAACATCTC,3470,,,,

current

Code:
chr9 21971208 CDKN2A c.151 1G>A p.?
chr9 21971209 CDKN2A c.151 2A>G p.?
chr5 112175216 112175216 APC p.E1309*
chr5 112175363 112175363 APC p.A1358T
chr5 112175390 112175390 APC p.Q1367*
chr7 55242470 55242487 EGFR c.2240_2257delTAAGAGAAGCAACATCTC p.L747_P753delinsS

desired

Code:
chr9 21971208 21971208 CDKN2A c.151-1G>A p.?
chr9 21971209 21971209 CDKN2A c.151-2A>G p.?
chr5 112175216 112175216 APC p.E1309*
chr5 112175363 112175363 APC p.A1358T
chr5 112175390 112175390 APC p.Q1367*
chr7 55242470 55242487 EGFR c.2240_2257delTAAGAGAAGCAACATCTC p.L747_P753delinsS

awk

Code:
awk -F'[ :_-]' 'NF==5{$4=$3;$3=$2} {$1=$1} 1' input


Last edited by cmccabe; 06-13-2019 at 07:24 PM..
 

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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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