Login or Register to Ask a Question and Join Our Community

Sponsored Content
Full Discussion: Perl to parse
Top Forums Shell Programming and Scripting Perl to parse Post 302939321 by cmccabe on Tuesday 24th of March 2015 04:34:42 PM
Old 03-24-2015
Perl to parse
The below code works great to parse out a file if the input is in the attached SNP format ">".

Code:
 perl -ne 'next if $.==1; while(/\t*NC_(\d+)\.\S+g\.(\d+)([A-Z])>([A-Z])/g){printf("%d\t%d\t%d\t%s\t%s\n",$1,$2,$2,$3,$4,$5)}' out_position.txt > out_parse.txt

My question is if there is another format in the input, such as "del" can both be parsed at the same time?

Code:
SNP parse rules (column 3 after the headr row is skipped):
1. 4 zeros after the NC_  (not always the case) and the digits before the .
2. g. ###   g.### (all digits)
3. letter (C) before the > 
4. letter (T) after the > 
Desired Output from parse:  13     20763438     20763438     C     G
Desired Output from parse: 13     20763642     20763642     C     G

DEL parse rules (column 3 after the headr row is skipped):
1. 4 zeros after the NC_  (not always the case) and the digits before the .
2. g. ###   g.### (all digits)
3. letter after "del" (C) 
4.  hyphen "-" used in this spot   
      
Desired Output from parse:  13     20763438     20763438     C     G

out_position.txt (483 Bytes) 
Last edited by cmccabe; 03-24-2015 at 05:53 PM..
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Perl parse string to time

Hi, I have got this value 18:21:23.330 in one of my variables. Now I need to parse this time to something. And then I have to compare it with 2 times, let's say, 15:00 hrs to 23:00 hrs. Can Date::Manip rescue me from this horrifying situation? I am quite new to Perl and especially this... (1 Reply)
Discussion started by: King Nothing
1 Replies

2. Shell Programming and Scripting

Perl Parse Word Cksum help

Hi all, I'm attempting to parse through a .bin file word by word and perform a cksum on each word using perl. I'm new to perl so I dont exactly know how to get started. Any help would be greatly appreciated. Thanks! (1 Reply)
Discussion started by: TeamUSA
1 Replies

3. Shell Programming and Scripting

perl parse line

Dear all anyone willling to help me..i have try so many time but still failed to get the ip address for line when i print the line is like below Connected to 192.168.1.13 #!/usr/local/bin/perl foreach $line(@lines){ if ($line =~ /connected to/) { $line=~/connected to(.*?) /; ... (2 Replies)
Discussion started by: netxus
2 Replies

4. Shell Programming and Scripting

Perl Parse

Hi I'm writing simple perl script to parse the ftp log as below: Local directory now /home/user/testing 227 Entering Passive Mode (192,254,19,34,8,228). 125 Data connection already open; Transfer starting. 09-25-09 02:33PM 25333629 abc.tar 09-14-09 12:50PM 18015752... (1 Reply)
Discussion started by: netxus
1 Replies

5. Shell Programming and Scripting

perl parse log

Hi anyone can help.how can i get all second column data in this log below?? x 799002577959.pdf, 25728 bytes, 51 tape blocks x 800002357216.pdf, 25728 bytes, 51 tape blocks x aadb090910.txt, 80424 bytes, 158 tape blocks x tsese090909.txt, 13974 bytes, 28 tape blocks (4 Replies)
Discussion started by: netxus
4 Replies

6. Shell Programming and Scripting

Parse file contents in perl...

Hi, I have the file like this: #Contents of file 1 are: Dec 10 12:33:44 User1 Interface: Probe Dec 10 12:33:47 uSER1 SOME DATA Dec 10 12:33:47 user1 Interface: MSGETYPE Dec 10 12:34:48 user1 ID: 10. Dec 10 12:33:55 user1 Interface: MSGTYPE Dec 10 12:33:55 user1 Id: 9 ... (1 Reply)
Discussion started by: vanitham
1 Replies

7. Shell Programming and Scripting

Perl parse error

Hello there, I em executing the following command in a perl script to append "\0" to the end of every line in a file: ###command start my $cmd = qx{"C:\\gawk" '{print $0 "\\\0"}' C:\file.txt > C:\file_1.txt}; ###command end But i get the following error: ###error meaasge start... (2 Replies)
Discussion started by: nmattam
2 Replies

8. Programming

Perl parse string

Hi Perl Guys I have another perl question I have the following code that i have written Getopt::Long::config(qw( permute bundling )); my $OPT = {}; GetOptions($OPT, qw( ver=s help|h )) or die "options parsing failed"; This will allow the user to do something like... (4 Replies)
Discussion started by: ab52
4 Replies

9. Shell Programming and Scripting

awk or perl to parse file

I have an input file attached that I am trying to parse in tab-delimanted format: The chromosomal variant column contains all the information: parse rules: 1. 4 zeros after the NC_ and the digits before the . 2. digits after the g. repeated twice separated by a tab 3. letter before the > 4.... (10 Replies)
Discussion started by: cmccabe
10 Replies

10. Shell Programming and Scripting

Help to parse syslog with perl

logver=56 idseq=63256900099118326 itime=1563205190 devid=FG-5KDTB18800138 devname=LAL-C1-FGT-03 vd=USER date=2019-07-15 time=18:39:49 logid="0000000013" type="traffic" subtype="forward" level="notice" eventtime=1563205189 srcip=11.3.3.17 srcport=50544 srcintf="SGI-CORE.123" srcintfrole="undefined"... (3 Replies)
Discussion started by: arm
3 Replies

LEARN ABOUT DEBIAN

locale::language

Locale::Language(3perl) 				 Perl Programmers Reference Guide				   Locale::Language(3perl)

NAME

       Locale::Language - standard codes for language identification

SYNOPSIS

	  use Locale::Language;

	  $lang = code2language('en');	      # $lang gets 'English'
	  $code = language2code('French');    # $code gets 'fr'

	  @codes   = all_language_codes();
	  @names   = all_language_names();

DESCRIPTION

       The "Locale::Language" module provides access to standard codes used for identifying languages, such as those as defined in ISO 639.

       Most of the routines take an optional additional argument which specifies the code set to use. If not specified, the default ISO 639 two-
       letter codes will be used.

SUPPORTED CODE SETS

       There are several different code sets you can use for identifying languages. The ones currently supported are:

       alpha-2
	   This is the set of two-letter (lowercase) codes from ISO 639, such as 'he' for Hebrew.

	   This code set is identified with the symbol "LOCALE_LANG_ALPHA_2".

	   This is the default code set.

       alpha-3
	   This is the set of three-letter (lowercase) bibliographic codes from ISO 639, such as 'heb' for Hebrew.

	   This code set is identified with the symbol "LOCALE_LANG_ALPHA_3".

       term
	   This is the set of three-letter (lowercase) terminologic codes from ISO 639.

	   This code set is identified with the symbol "LOCALE_LANG_TERM".

ROUTINES

       code2language ( CODE [,CODESET] )
       language2code ( NAME [,CODESET] )
       language_code2code ( CODE ,CODESET ,CODESET2 )
       all_language_codes ( [CODESET] )
       all_language_names ( [CODESET] )
       Locale::Language::rename_language  ( CODE ,NEW_NAME [,CODESET] )
       Locale::Language::add_language  ( CODE ,NAME [,CODESET] )
       Locale::Language::delete_language  ( CODE [,CODESET] )
       Locale::Language::add_language_alias  ( NAME ,NEW_NAME )
       Locale::Language::delete_language_alias	( NAME )
       Locale::Language::rename_language_code  ( CODE ,NEW_CODE [,CODESET] )
       Locale::Language::add_language_code_alias  ( CODE ,NEW_CODE [,CODESET] )
       Locale::Language::delete_language_code_alias  ( CODE [,CODESET] )
	   These routines are all documented in the Locale::Codes man page.

SEE ALSO

       Locale::Codes
       Locale::Constants
       http://www.loc.gov/standards/iso639-2/
	   Source of the ISO 639 codes.

AUTHOR

       See Locale::Codes for full author history.

       Currently maintained by Sullivan Beck (sbeck@cpan.org).

COPYRIGHT

	  Copyright (c) 1997-2001 Canon Research Centre Europe (CRE).
	  Copyright (c) 2001-2010 Neil Bowers
	  Copyright (c) 2010-2011 Sullivan Beck

       This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

perl v5.14.2							    2011-09-26						   Locale::Language(3perl)
All times are GMT -4. The time now is 10:45 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy