Is it possible to rename fasta headers based on its position specified in another file? Post: 303041047

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Merging of files with different headers to make combined headers file

Hi , I have a typical situation. I have 4 files and with different headers (number of headers is varible ). I need to make such a merged file which will have headers combined from all files (comman coluns should appear once only). For example - File 1 H1|H2|H3|H4 11|12|13|14 21|22|23|23...

2. UNIX for Dummies Questions & Answers

To Extract words from File based on Position

Hi Guys, While I was writing one shell script , I just got struck at this point. I need to extract words from a file at some specified position and do some comparison operation and need to replace the extracted word with another word. Eg : I like Orange very much. I need to replace...

3. UNIX for Dummies Questions & Answers

Script to delete a word based on position in a file

Hi, I am new to unix. I want to delete 2 words placed at position say for example at 23rd and 45th position in a line. I used sed but couldnt achieve this. Example: the file contains 2 lines 12345 98765 "12345" 876 12345 98765 "64578" 876 I want to delete " placed at position 13 and 19...

4. Shell Programming and Scripting

Replacing headers based on a second file

I have a file with thousands of sequences that looks like this: I need to replace the headers using a second file Thus, I will end up having the following file: I am looking for an AWK script that I can easily plug in my current pipeline. Any help will be greatly appreciated!

5. UNIX for Dummies Questions & Answers

extract regions of file based on start and end position

Hi, I have a file1 of many long sequences, each preceded by a unique header line. file2 is 3-columns list: headers name, start position, end position. I'd like to extract the sequence region of file1 specified in file2. Based on a post elsewhere, I found the code: awk...

6. Shell Programming and Scripting

Fixed width file search based on position value

Hi, I am unable to find the right option to extract the data in the fixed width file. sample data abcd1234xgyhsyshijfkfk hujk9876 io xgla loki8787eljuwoejroiweo dkfj9098 dja Search based on position 8-9="xg" and print the entire row output ...

7. Shell Programming and Scripting

Split file based on distinct value at specific position

OS : Linux 2.6x Shell : Korn In a single file , how can I identify all the Uniqe values at a specific character position and length of each record , and simultaneously SPLIT the records of the file based on each of these values and write them in seperate files . Lets say : a) I want to...

8. Shell Programming and Scripting

Extract sequences from a FASTA file based on another file

9. UNIX for Dummies Questions & Answers

Append file name to fasta file headers in Linux

How do we append the file name to fasta file headers in multiple fasta-files in Linux?

10. Shell Programming and Scripting

Search for a string at a particular position and replace with blank based on position

Hi, I have a file with multiple lines(fixed width dat file). I want to search for '02' in the positions 45-46 and if available, in that lines, I need to replace value in position 359 with blank. As I am new to unix, I am not able to figure out how to do this. Can you please help me to achieve...

LEARN ABOUT OSX

locale::codes::langfam

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

NAME

       Locale::Codes::LangFam - standard codes for language extension identification

SYNOPSIS

	  use Locale::Codes::LangFam;

	  $lext = code2langfam('apa');		       # $lext gets 'Apache languages'
	  $code = langfam2code('Apache languages');    # $code gets 'apa'

	  @codes   = all_langfam_codes();
	  @names   = all_langfam_names();

DESCRIPTION

       The "Locale::Codes::LangFam" module provides access to standard codes used for identifying language families, such as those as defined in
       ISO 639-5.

       Most of the routines take an optional additional argument which specifies the code set to use. If not specified, the default ISO 639-5
       language family codes will be used.

SUPPORTED CODE SETS

       There are several different code sets you can use for identifying language families. 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 = code2langfam('apa','alpha');
	  $lext = code2langfam('apa',LOCALE_LANGFAM_ALPHA);

       The codesets currently supported are:

       alpha
	   This is the set of three-letter (lowercase) codes from ISO 639-5 such as 'apa' for Apache languages.

	   This is the default code set.

ROUTINES

       code2langfam ( CODE [,CODESET] )
       langfam2code ( NAME [,CODESET] )
       langfam_code2code ( CODE ,CODESET ,CODESET2 )
       all_langfam_codes ( [CODESET] )
       all_langfam_names ( [CODESET] )
       Locale::Codes::LangFam::rename_langfam  ( CODE ,NEW_NAME [,CODESET] )
       Locale::Codes::LangFam::add_langfam  ( CODE ,NAME [,CODESET] )
       Locale::Codes::LangFam::delete_langfam  ( CODE [,CODESET] )
       Locale::Codes::LangFam::add_langfam_alias  ( NAME ,NEW_NAME )
       Locale::Codes::LangFam::delete_langfam_alias  ( NAME )
       Locale::Codes::LangFam::rename_langfam_code  ( CODE ,NEW_CODE [,CODESET] )
       Locale::Codes::LangFam::add_langfam_code_alias  ( CODE ,NEW_CODE [,CODESET] )
       Locale::Codes::LangFam::delete_langfam_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.loc.gov/standards/iso639-5/id.php
	   ISO 639-5 .

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::LangFam(3pm)

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Merging of files with different headers to make combined headers file

Discussion started by: marut_ashu

2. UNIX for Dummies Questions & Answers

To Extract words from File based on Position

Discussion started by: kuttu123

3. UNIX for Dummies Questions & Answers

Script to delete a word based on position in a file

Discussion started by: nbks2u

4. Shell Programming and Scripting

Replacing headers based on a second file

Discussion started by: Xterra