After a bash function is run the below file is produced:
out_name.txt tab-delimeted
Code:
Input Errors and warnings AccNo Genesymbol Variant Reference Sequence Start Descr. Coding DNA Descr. Protein Descr. GeneSymbol Coding DNA Descr. GeneSymbol Protein Descr. Genomic Reference Coding Reference Protein Reference Affected Transcripts Affected Proteins Restriction Sites Created Restriction Sites Deleted
NM_003924.3:c.242-1G>A (variantchecker): Intronic position given for a non-genomic reference sequence.
NM_003924.3:c.*18_*19delGCinsAA NM_003924.3 PHOX2B_v001 c.*18_*19delGCinsAA n.1323_1324delinsAA c.*18_*19delinsAA p.(=) PHOX2B_v001:c.*18_*19delinsAA PHOX2B_v001:p.(=) NM_003924.3 NP_003915.2 NM_003924.3(PHOX2B_v001):c.*18_*19delinsAA NM_003924.3(PHOX2B_i001):p.(=) HpyAV
NM_003924.3:c.013G>T NM_003924.3 PHOX2B_v001 c.013G>T n.373G>T c.13G>T p.(Glu5*) PHOX2B_v001:c.13G>T PHOX2B_v001:p.(Glu5*) NM_003924.3 NP_003915.2 NM_003924.3(PHOX2B_v001):c.13G>T NM_003924.3(PHOX2B_i001):p.(Glu5*)
I am trying to add a condition that will suppress the warning message produced if $2 is (variantchecker): Intronic position given for a non-genomic reference sequence.,
In addition, that the $1 string "is an intronic variant" is displayed instead of the waring. My 2nd attempt to incorporate these changes is below,
which executes but nothing results. Thank you .
desired result
Code:
NM_003924.3:c.242-1G>A is an intronic variant
awk
Code:
while read LINE; do
awk -F'\t' '$2 == "variantchecker): Intronic position given for a non-genomic reference sequence." {print $1 && "is an intronic variant"}' 2>/dev/null
done < out_name.txt
Last edited by cmccabe; 03-09-2017 at 01:11 PM..
Reason: fixed format
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LEARN ABOUT OSX
locale::codes::langvar
Locale::Codes::LangVar(3pm) Perl Programmers Reference Guide Locale::Codes::LangVar(3pm)NAME
Locale::Codes::LangVar - standard codes for language variation identification
SYNOPSIS
use Locale::Codes::LangVar;
$lvar = code2langvar('acm'); # $lvar gets 'Mesopotamian Arabic'
$code = langvar2code('Mesopotamian Arabic'); # $code gets 'acm'
@codes = all_langvar_codes();
@names = all_langvar_names();
DESCRIPTION
The "Locale::Codes::LangVar" module provides access to standard codes used for identifying language variations, 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 variations. 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:
$lvar = code2langvar('en','alpha-2');
$lvar = code2langvar('en',LOCALE_CODE_ALPHA_2);
The codesets currently supported are:
alpha
This is the set of alphanumeric codes from the IANA language registry, such as 'arevela' for Eastern Armenian.
This code set is identified with the symbol "LOCALE_LANGVAR_ALPHA".
This is the default code set.
ROUTINES
code2langvar ( CODE [,CODESET] )
langvar2code ( NAME [,CODESET] )
langvar_code2code ( CODE ,CODESET ,CODESET2 )
all_langvar_codes ( [CODESET] )
all_langvar_names ( [CODESET] )
Locale::Codes::LangVar::rename_langvar ( CODE ,NEW_NAME [,CODESET] )
Locale::Codes::LangVar::add_langvar ( CODE ,NAME [,CODESET] )
Locale::Codes::LangVar::delete_langvar ( CODE [,CODESET] )
Locale::Codes::LangVar::add_langvar_alias ( NAME ,NEW_NAME )
Locale::Codes::LangVar::delete_langvar_alias ( NAME )
Locale::Codes::LangVar::rename_langvar_code ( CODE ,NEW_CODE [,CODESET] )
Locale::Codes::LangVar::add_langvar_code_alias ( CODE ,NEW_CODE [,CODESET] )
Locale::Codes::LangVar::delete_langvar_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) 2011-2012 Sullivan Beck
This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
perl v5.16.2 2012-10-11 Locale::Codes::LangVar(3pm)
03-09-2017
.