Login or Register to Ask a Question and Join Our Community

Sponsored Content
Full Discussion: Need help comparing Base Pairs within PERL
Top Forums Shell Programming and Scripting Need help comparing Base Pairs within PERL Post 302651327 by drossy on Tuesday 5th of June 2012 10:23:18 AM
Old 06-05-2012
Yes sorry for not specifying more.
Say the given reference was:
Code:
 
Index 
1)T
2)A
3)C
4)G
5)C

and that the matix in my first post remains the same, indexes 3 and 4 would not have an allele in their genotype that matches that of the reference for that position. My desired output in this situation would be:

Code:
 
3   Chr1   Exonic
4   Chr1   Frameshift

I hope this explanation is more useful.
Thanks again
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

perl search and replace pairs

Hello all im facing some kind of problem i have this string : functionA() $" "$ functionB("arg1") $" = "$ i will like to replace all the pairs of opening and closing "$" to be something like that functionA() <#" "#> functionB("arg1") <#" = "#> i cant of course do is with simple ... (1 Reply)
Discussion started by: umen
1 Replies

2. Shell Programming and Scripting

Comparing Variables in Perl

Hi. I have three arrays. @a=('AB','CD','EF'); @b=('AB,'DG',HK'); @c=('DD','TT','MM'); I want to compare the elements of the first two array and if they match then so some substition. I tried using the if statement using the scalar value of the array but its not giving me any output. ... (7 Replies)
Discussion started by: kamitsin
7 Replies

3. Shell Programming and Scripting

Comparing arrays in perl

Hi all, I am trying to compare two arrays in perl using the following code. foreach $item (@arrayA){ push(@arrayC, $item) unless grep(/$item/, @arrayB); ... (1 Reply)
Discussion started by: chriss_58
1 Replies

4. Shell Programming and Scripting

PERL name value pairs substituions

I have a main file with variable tokens like this: name: File1 =========== Destination/Company=@deploy.company@ Destination/Environment=@deploy.env@ Destination/Location=@deploy.location@ Destination/Domain=@deploy.location@ MIG_GatewayAddresses=@deploy.gwaddress@ MIG_URL=@deploy.mig_url@... (1 Reply)
Discussion started by: uandme2k2
1 Replies

5. Shell Programming and Scripting

comparing list values in Perl

Hi, I have tab separated list: KB0005 1019 T IFVATVPVI 0.691 PKC YES KB0005 1036 T YFLQTSQQL 0.785 PKC YES KB0005 1037 S FLQTSQQLK 0.585 DNAPK YES KB0005 508 S ENIISGVSY 0.507 cdc2 YES KB0005 511 S ... (1 Reply)
Discussion started by: karla
1 Replies

6. Shell Programming and Scripting

PERL: simple comparing arrays question

Hi there, i have been trying different methods and i wonder if somebody could explain to me how i would perform a comparison on two arrays for example my @array1 = ("gary" ,"peter", "paul"); my @array2 = ("gary" ,"peter", "joe"); I have two arrays above, and i want to something like this... (5 Replies)
Discussion started by: hcclnoodles
5 Replies

7. Shell Programming and Scripting

Perl: Comparing to two files and displaying the differences

Hi, I'm new to perl and i have to write a perl script that will compare to log/txt files and display the differences. Unfortunately I'm not allowed to use any complied binaries or applications like diff or comm. So far i've across a code like this: use strict; use warnings; my $list1;... (2 Replies)
Discussion started by: dont_be_hasty
2 Replies

8. Shell Programming and Scripting

Perl: Need help comparing huge files

What do i need to do have the below perl program load 205 million record files into the hash. It currently works on smaller files, but not working on huge files. Any idea what i need to do to modify to make it work with huge files: #!/usr/bin/perl $ot1=$ARGV; $ot2=$ARGV; open(mfileot1,... (12 Replies)
Discussion started by: mrn6430
12 Replies

9. Shell Programming and Scripting

Need help in comparing two files using shell or Perl

I have these two file that I am trying to compare using shell arrays. I need to find out the changed or the missing enteries from File2. For example. The line "f nsd1" in file2 is different from file1 and the line "g nsd6" is missing from file2. I dont want to use "for loop" because my files... (2 Replies)
Discussion started by: sags007_99
2 Replies

10. Shell Programming and Scripting

Perl for comparing numbers from previous lines in a file?

Hi everyone I have a question for you, as I am trying to learn more about Perl and work with some weather data. I have an ascii file (shown below) that has 10 lines with different columns. What I would like is have Perl find an "anomalous" value by comparing a field with the values from the last... (2 Replies)
Discussion started by: lucshi09
2 Replies

LEARN ABOUT OSX

locale::codes::langext

Locale::Codes::LangExt(3pm)				 Perl Programmers Reference Guide			       Locale::Codes::LangExt(3pm)

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) 2011-2012 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::LangExt(3pm)
All times are GMT -4. The time now is 10:54 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy