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Full Discussion: Fasta header modification
Top Forums UNIX for Dummies Questions & Answers Fasta header modification Post 302922933 by Lokaps on Wednesday 29th of October 2014 08:41:48 AM
Old 10-29-2014
Fasta header modification

Hi,

I need some help with modifying fasta headers.

I have a fasta file with thousands of contigs and I need to modify their headers with the information obtained from a second file.


File 1 contains the fasta sequences:
Code:
>contig0001 length=11115 numreads=10777
agatgtagatctct
>contig0002 lenth=23412 numreads=2345
atcgtcat

File 2 contains the information that I need to add to each header:
Code:
1 contig0001 11115 20.5
2 contig0002 23412 13.5

The output file should look like:
Code:
>contig0001_11115_[cov=20.5]
agatgtagatctct
>contig0002_23412_[cov=13.5]
atcgtcat


Thanks.
 

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

NAME
Locale::Codes::LangVar - standard codes for language variation identification SYNOPSIS
use Locale::Codes::LangVar; $lvar = code2langvar('acm'); # $lvar gets 'Mesopotamian Arabic' $code = langvar2code('Mesopotamian Arabic'); # $code gets 'acm' @codes = all_langvar_codes(); @names = all_langvar_names(); DESCRIPTION
The "Locale::Codes::LangVar" module provides access to standard codes used for identifying language variations, 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 variations. 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: $lvar = code2langvar('en','alpha-2'); $lvar = code2langvar('en',LOCALE_CODE_ALPHA_2); The codesets currently supported are: alpha This is the set of alphanumeric codes from the IANA language registry, such as 'arevela' for Eastern Armenian. This code set is identified with the symbol "LOCALE_LANGVAR_ALPHA". This is the default code set. ROUTINES
code2langvar ( CODE [,CODESET] ) langvar2code ( NAME [,CODESET] ) langvar_code2code ( CODE ,CODESET ,CODESET2 ) all_langvar_codes ( [CODESET] ) all_langvar_names ( [CODESET] ) Locale::Codes::LangVar::rename_langvar ( CODE ,NEW_NAME [,CODESET] ) Locale::Codes::LangVar::add_langvar ( CODE ,NAME [,CODESET] ) Locale::Codes::LangVar::delete_langvar ( CODE [,CODESET] ) Locale::Codes::LangVar::add_langvar_alias ( NAME ,NEW_NAME ) Locale::Codes::LangVar::delete_langvar_alias ( NAME ) Locale::Codes::LangVar::rename_langvar_code ( CODE ,NEW_CODE [,CODESET] ) Locale::Codes::LangVar::add_langvar_code_alias ( CODE ,NEW_CODE [,CODESET] ) Locale::Codes::LangVar::delete_langvar_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 v5.18.2 2014-01-06 Locale::Codes::LangVar(3pm)
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