The value to update is only a - or +, I apologize for any typo.
Here is how I read the awk, which is much closer than mine . Thank you very much .
Code:
awk # Invoke awk
FNR==NR # For each line in the 1st input file (file)...
{A[$2]=$3 # Assign each name in field 2 = to the value in field 3 them to array A
;next} # Process next line and end block
($9 ~ /-[0-9]+$|+[0-9]+$/) # Check if field 9 in out has a - or = in it
{Q=$8; # If it does read the contents of the matching field 8 into array Q
or(Q in A){$9=$9 # For each matching array Q in array A
":"A[Q]};print # print the updated line with the updated NM_ seperated with a :
OFS="\t" # Add a tab to the output
' file out > new # Define input and output
Code:
awk 'FNR==NR{A[$2]=$3;next} ($9 ~ /-[0-9]+$|+[0-9]+$/){Q=$8;for(Q in A){$9=$9":"A[Q]};print}' OFS="\t" file out > new
current new (just the 3 updated lines with multiple NM_)
Code:
1 chr1 948846 948846 - A upstream ISG15 -0:NM_005101.3:NM_024027.4:NM_001111.4:NM_001006658.2 . . .
4 chr1 949925 949925 C T downstream ISG15 +6:NM_005101.3:NM_024027.4:NM_001111.4:NM_001006658.2 . . .
8 chr1 948840 948840 - C upstream ISG15 -6:NM_005101.3:NM_024027.4:NM_001111.4:NM_001006658.2 . . .
desired new (all lines printed but only the 3 from above are updated with an :NM_
Code:
R_Index Chr Start End Ref Alt Func.IDP.refGene Gene.IDP.refGene GeneDetail.IDP.refGene Inheritence ExonicFunc.IDP.refGene AAChange.IDP.refGene
1 chr1 948846 948846 - A upstream ISG15 -0:NM_005101.3 . . .
2 chr1 948870 948870 C G UTR5 ISG15 NM_005101.3:c.-84C>G . .
4 chr1 949925 949925 C T downstream ISG15 +6:NM_005101.3 . . .
5 chr1 207646923 207646923 G A intronic CR2 >50 . . .
8 chr1 948840 948840 - C upstream ISG15 -6:NM_005101.3 . . .
Hi All,
I have a data file which has two columns Location and the Count.
The file looks like this
India 1
US 0
UK 2
China 0
What I have to do is whenever I fails to login to Oracle then I have to add 1 to the count for that location.
Whenever my script fails to login to Oracle for a... (5 Replies)
Hello, wondering if anybody may be help me. This is the output of a file, from which I need to display a number of fields regarding which users are using licences for two applications we run. Lines which end with "(linger: 1800)" denote licence use for one application and lines which don't contain... (8 Replies)
Look at this simple example.
echo " 2 4 6" | awk '{$2+=3;$3-=1}1'
2 7 5
Is there a simple way to update a field and at the same time keep the formatting?
I would like to get it like this
2 7 5
I have tested both sub and gsub, it reformat too. (2 Replies)
If $1 in file1 matches $2 in file2. Then the value in $2 of file2 is updated to $1"."$2 of file2. The awk seems to only match the two files but not update. Thank you :).
awk
awk 'NR==FNR{A ; next} $1 in A { $2 = a }1' file1 file2
file1
name version
NM_000593 5
NM_001257406... (3 Replies)
I am trying to match $1 in file1 with $2 in file2. If a match is found then $3 and $4 of file2 are copied to file1. Both files are tab-delimeted and I am getting a syntax error and would also like to update file1 in-place without creating a new file, but am not sure how. Thank you :).
file1
... (19 Replies)
I am trying to use awk to match two files that are tab-delimited. When a match is found between file1 $1 and file2 $4, $4 in file2 is updated using the $2 value in file1. If no match is found then the next line is processed. Thank you :).
file1
uc001bwr.3 ADC
uc001bws.3 ADC... (4 Replies)
In the tab-delimeted input file below I am trying to use awk to update the value in $2 if TYPE=ins in bold, by adding the value of
HRUN= in italics. In the below since in line 1 TYPE=ins the 117282541 value in $2 has 6 added because that is the value of HRUN=.
Hopefully the awk is a start but I... (2 Replies)
Trying to use awk to:
update $2 in file2 with the $2 value in file1, if $1 in file1 matches $13 in file2, which is tab-delimeted. The $2values may already be the same so in that case nothing happens and the next line is processed.
There are exactly 4,605 unique $13 values. Thank you :).
... (4 Replies)
In the awk below I am trying to set/update the value of $14 in file2 in
bold, using the matching NM_ in $12 or $9 in file2
with the NM_ in $2 of file1.
The lengths of $9 and $12 can be variable but what is consistent is the start pattern
will always be NM_ and the end pattern is always ;... (2 Replies)
In the awk below I am trying to copy the entire contents of $6 there may be multiple values seperated by a ;, to $8, if $8 is . (lines 1 and 3 are examples). If that condition $8 is not . (line2 is an example) then that line is skipped and printed as is. The awk does execute but prints the output... (3 Replies)
Discussion started by: cmccabe
3 Replies
LEARN ABOUT MOJAVE
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) 2011-2013 Sullivan Beck
This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
perl v5.18.2 2014-01-06 Locale::Codes::LangVar(3pm)
04-05-2017
. Thank you very much