Login or Register to Ask a Question and Join Our Community

Sponsored Content
Full Discussion: how to fetch substring from records into another file
Top Forums Shell Programming and Scripting how to fetch substring from records into another file Post 302220290 by aigles on Thursday 31st of July 2008 10:04:49 AM
Old 07-31-2008
I am not sure that the output of the following script is what what you are looking for.
Try and adapt it.
Code:
awk -F'\t' '

NR==FNR {
   if (NR==1)
      Key_len = length($1) + 1;
   k = ">" substr($0,1, Key_len-1);
   n = ++Keys[k];
   From[k,n] = $2;
     To[k,n] = $3;
    Len[k,n] = $3 - $2;
   next;
}

function print_selected(    i,k) {
   if (selected) {
      k = substr(Header, 1, Key_len);
      for (i=1; i<=Keys[k]; i++) {
         printf("%s (%s-%s)\n", Header, From[k,i], To[k,i]);
         print substr(Alphabets, From[k,i], Len[k,i]);
      }
   }
}

/^>/ {
   print_selected();
   selected  = (substr($0, 1, Key_len) in Keys);
   Header    = $0;
   Alphabets = "";
   next;
}

selected {
   Alphabets = Alphabets $0;
}

END {
   print_selected();
}
' FILE2 FILE1

Input file FIL1 :
Code:
>bi|2138271|geb|AAC15885.1|precursor [Sambucus nigra]
MRVIAAAMLYLYIVVLAICSVGIQGIDYPSVSFNLAGAKSATWDFLRMPHDLVGEDNKYNDGEPITGNII
GRDGLCVDVRNGYDTDGTPLQLWPCGTQRNQQWTFYTDDTIRSMGKCMTANGLSNGSNIMIFNCSTAVEN
AIKWEVTIDGSIINPSSG
>bi|21083|em|CAA26939.1| precursor [Ricinus communis]
MKPGGNTIVIWMYAVATWLCFGSTSGWSFTLEDNNIFPKQYPIINFTTAGATVQSYTNFIRAVRGRLTTG
ADVRHEIPVLPNRVGLPINQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAIT
HLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTL
>bi|19526601|geb|AAL87006.1| chain A [Viscum album]
YERLRLRVTHQTTGEEYFRFITLLRDYVSSGSFSNEIPLLRQSTIPVSDAQRFVLVELTNEGGDSITAAI
DVTNLYVVAYQAGDQSYFLRDAPRGAETHLFTGTTRSSLPFNGSYPDLERYAGHRDQIPLGIDQLIQSVT
ALRFPGGNTRTQARSILILIQMISEAARFNPILWRARQYINSGASFLPDVY

Input file FILE2 :
Code:
bi|2138271|geb|AAC15885 20      32
bi|2138271|geb|AAC15885 92      110
bi|19526601|geb|AAL8700 74      92
bi|2138271|geb|AAC15885 26      38
bi|21083|em|CAA26939.1| 19      37
bi|21083|em|CAA26939.1| 52      70

Output:
Code:
>bi|2138271|geb|AAC15885.1|precursor [Sambucus nigra] (20-32)
SVGIQGIDYPSV
>bi|2138271|geb|AAC15885.1|precursor [Sambucus nigra] (92-110)
LWPCGTQRNQQWTFYTDD
>bi|2138271|geb|AAC15885.1|precursor [Sambucus nigra] (26-38)
IDYPSVSFNLAG
>bi|21083|em|CAA26939.1| precursor [Ricinus communis] (19-37)
LCFGSTSGWSFTLEDNNI
>bi|21083|em|CAA26939.1| precursor [Ricinus communis] (52-70)
TVQSYTNFIRAVRGRLTT
>bi|19526601|geb|AAL87006.1| chain A [Viscum album] (74-92)
NLYVVAYQAGDQSYFLRD

Jean-Pierre.
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Count No of Records in File without counting Header and Trailer Records

I have a flat file and need to count no of records in the file less the header and the trailer record. I would appreciate any and all asistance Thanks Hadi Lalani (2 Replies)
Discussion started by: guiguy
2 Replies

2. Shell Programming and Scripting

fetch substring from html code

hello mates. please help me out once again. i have a html file where i want to fetch out one value from the entire html-code sample html code: ..... <b>Amount:<b> 12345</div> ... now i only want to fetch the 12345 from the html document. how to i tell sed to get me the value from... (2 Replies)
Discussion started by: scarfake
2 Replies

3. Shell Programming and Scripting

Fetch lines from a file matching column2 of another file

Hi guys, Please help me out in this problem. I have two files FILE1 abc-23 : 4529675 cde-42 : 9824532 dge-91 : 1245367 gre-45 : 9824532 fgr-76 : 4529675 FILE2 4529675 : Gal Glu house-2-be 9824532 : cat mouse 1245367 : sirf surf-2-beta where FILE2 is a static file with fixed... (5 Replies)
Discussion started by: smriti_shridhar
5 Replies

4. Shell Programming and Scripting

how to scan a sequential file to fetch some of the records?

Hi I am working on a script which needs to scan a sequential file and fetch the row where 2nd column = 'HUB' Can any one help me with this... Thanks (1 Reply)
Discussion started by: manmeet
1 Replies

5. Shell Programming and Scripting

How to sca a sequential file and fetch some substring data from it

Hi, I have a task where i need to scan second column of seuential file and fetch first 3 digits of that column For e.g. FOLLOWING IS THE SAMPLE FOR MY SEQUENTIAL FILE AU_ID ACCT_NUM CRNCY_CDE THHSBC001 30045678 THB THHSBC001 10154267 THB THHSBC001 ... (2 Replies)
Discussion started by: manmeet
2 Replies

6. UNIX for Dummies Questions & Answers

Grep specific records from a file of records that are separated by an empty line

Hi everyone. I am a newbie to Linux stuff. I have this kind of problem which couldn't solve alone. I have a text file with records separated by empty lines like this: ID: 20 Name: X Age: 19 ID: 21 Name: Z ID: 22 Email: xxx@yahoo.com Name: Y Age: 19 I want to grep records that... (4 Replies)
Discussion started by: Atrisa
4 Replies

7. Shell Programming and Scripting

make the name of file and fetch few things from log file

Hello All, I am working on a script where I need to fetch the value from a log file and log file creates with different name but few thing are common DEV_INFOMGT161_MULTI_PTC_BLD01.Stage_All_to_stp2perf1.042312114644.log STP_12_02_01_00_RC01.Stage_stp-domain_to_stp2perf2.042312041739.log ... (2 Replies)
Discussion started by: anuragpgtgerman
2 Replies

8. Shell Programming and Scripting

Deleting duplicate records from file 1 if records from file 2 match

I have 2 files "File 1" is delimited by ";" and "File 2" is delimited by "|". File 1 below (3 record shown): Doc1;03/01/2012;New York;6 Main Street;Mr. Smith 1;Mr. Jones Doc2;03/01/2012;Syracuse;876 Broadway;John Davis;Barbara Lull Doc3;03/01/2012;Buffalo;779 Old Windy Road;Charles... (2 Replies)
Discussion started by: vestport
2 Replies

9. Shell Programming and Scripting

Separate records of a file on 2 types of records

Hi I am new to shell programming in unix Please if I can provide help. I have a file structure of a header record and "N" detail records. The header record will be the total number of detail records I need to split the file in 2: One for the header Another for all detail records Could... (1 Reply)
Discussion started by: jamcogar
1 Replies

10. Shell Programming and Scripting

How to fetch matched records from files between two different directory?

awk 'NR==FNR{arr;next} $0 in arr' /tmp/Data_mismatch.sh /prd/HK/ACCTCARD_20160115.txt edit by bakunin: seems that one CODE-tag got lost somewhere. i corrected that, but please check your posts more carefully. Thank you. (5 Replies)
Discussion started by: suresh_target
5 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)
All times are GMT -4. The time now is 04:04 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy