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Top Forums UNIX for Beginners Questions & Answers How to append two fasta files? Post 303036081 by Scrutinizer on Thursday 13th of June 2019 05:03:02 PM
Old 06-13-2019
Post #7 probably did not work for you because there are excess trailing spaces that need to be removed in the file samples, but that are not going to be present in the actual FASTA files, see the note underneath...

--
Here they are without the spaces:
File1:
Code:
>Contig_1:90600-91187
GACCGTCATCAATTCCTGTTCCTTGCCCTTGACGACCTCATCCACGTCCTTGATGGCCTT
>Contig_24:26615-28387
TTCGCCGCGCTCCAAACGGGCGATCTCCTCGGCGCGGGCCGCCAGGATCAGCGCCG
>Contig_98:35323-35886
GACGAAGCGCTCGCCAAGGCCGAAGAAGAAGGCCTGGATCTGGTCGAAATCCAGCCGCAG               
AAGGCCATCAAGGACGTGGATGAGGTCGTCAAGGGCAAGGA

File2:
Code:
>Contig_1:90600-91187
AAGGCCATCAAGGACGTGGATGAGGTCGTCAAGGGCAAGGAACAGGAATTGATGACGGTC
AAGGCCATCAAGGACGTGGATGAGGTCGTCAAGGGCAAGGAACAGG
AAGGCCATCAAGGACGTGGATGAGGTCGTCAAGGGCAAGGA
>Contig_24:26615-28387
GCTGCGGCGCTGATCCTGGCGGCCCGCGCCGAGGAGATCGCCCGTTTGGAGCGCGGCGAA

Of course another thing is the order that is mixed up when because it is undefined in the array structure in awk. That could easily be fixed of course if need be.

Last edited by Scrutinizer; 06-13-2019 at 06:12 PM..
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Locale::Codes::LangVar(3)				User Contributed Perl Documentation				 Locale::Codes::LangVar(3)

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('arevela','alpha'); $lvar = code2langvar('arevela',LOCALE_LANGVAR_ALPHA); 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 v5.16.3 2013-04-12 Locale::Codes::LangVar(3)
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