awk script to parse case with information in two fields of file
The below awk parser works for most data inputs, but I am having trouble with the last one. The problem is in the below rules steps 1 and 2 come from $2 (NC_000013.10:g.20763686_20763687delinsA) and steps 3 and 4 come from $1 (NM_004004.5:c.34_35delGGinsT).
Code:
Parse Rules:
The header is skipped and
1. 4 zeros after the NC_ (not always the case) and the digits before the .
2. g. ### (before underscore) _### (# after the _)
3. letters after the "del" until the “ins”
4. letters after the "ins"
Desired output: 13 20763686 20763687 GG T
suppose if u have a file like that
Hen ABCCSGSGSGJJJJK 15
Cock ABCCSGGGSGIJJJL 15
* * * * * * : * * * . * * * :
Hen CFCDFCSDFCDERTF 30
Cock CHCDFCSDHCDEGFI 30
* . * * * * * * * : * * :* : : .
The output shud be
where there is : and .
It shud... (4 Replies)
I have a file name version.properties with the following data:
major.version=14
minor.version=234
I'm trying to write a grep expression to only put "14" to stdout. The following is not working.
grep "major.version=(+)" version.properties
What am I doing wrong? (6 Replies)
Hi everyone,
I'm trying to use the "join" function for more than 1 field. Since it's not possible as it is, I want to take my input files and concatenate the joining fields as 1 field (separated by "|"). I wrote 2 awk script to do and undo it (see below). However I'm new to awk and I'm certain I... (5 Replies)
When parsing multiple fields in a file using AWK, how do you group by one of the fields and parse by delimiters?
to clarify
If a file had
tom | 223-2222-4444 , randofield
ivan | 123-2422-4444 , random filed
... | and , are the delimiters ...
How would you group by the social security... (4 Replies)
Hi,
I want to split/parse certain bits of the hex data into another field.
Example:
Input data is
Word1: 4f72abfd
Output:
Parse bits (5 to 0) into field word1data1=0x00cd=205 decimal
Parse bits (7 to 6) into field word1data2=0x000c=12 decimal
etc.
Word2: efff3d02
Parse bits (13 to... (1 Reply)
Hello,
I have a log file , i want to delete the lines of the log file which is match with 1st and 5th field with different patterns. Once it will meet with that condition it will delete that line from the log . I dont want to create any temp file over there.
Successfully able to retrieve the... (1 Reply)
Hi Unix gurus..
I have a file which has below data, It has several MQ Queue statistics;
QueueName= 'TEST1'
CreateDate= '2009-10-30'
CreateTime= '13.45.40'
QueueType= Predefined
QueueDefinitionType= Local
QMinDepth= 0
QMaxDepth= 0
QueueName= 'TEST2'
CreateDate= '2009-10-30'... (6 Replies)
I have a special case that awk could be used but I do not have the skill. Trying to create a final output file (indel_parse.txt) that is created from using some information from each of the two files (attached).
parse rules:
The header is skipped FNR>1
1. 4 zeros after the NC_ (not... (2 Replies)
Hello,
I am working parsing a large input file1(field CFA)
I have to compare the the file1 field(CFA byte 88-96) with the content of the file2(It contains only one field) and and insert rows equal
in another file.
Here is my code and sample input file:
... (7 Replies)
I have a file of ~500,000 entries in the following:
file.txt
chr1 11868 12227 ENSG00000223972.5 . + HAVANA exon . gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type... (17 Replies)
Discussion started by: cmccabe
17 Replies
LEARN ABOUT CENTOS
locale::codes::langext
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)
04-08-2015
.