Hi,
I'm in need of creating a file in the fasta format:
>1A6A.A
HVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITN
VPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCR
VEHWGLDEPLLKHWEF
>1A6A.B ... (5 Replies)
Hi All, I need to grep few files which has words like the below in the file name , which i want to put it in a file and and grep for the files which contain these names and move it to a new directory ,
full file name -C20091210.1000-20091210.1100_SMGBSC3:1000... (2 Replies)
I really need some help with this task. I have a bunch of FASTA files with hundreds of DNA sequences that look like this:
>SeqID1
AACCATGACAGAGGAGATGTGAACAGATAGAGGGATGACAGATGACAGATAGACCCAGAC
TGACAGGTTCAAAGGCTGCAGTGCAGTGACGTGACGATTT
>Sequence 22... (13 Replies)
I have a fasta file that looks like this:
>Noname
ACCAAAATAATTCATGATATACTCAGATCCATCTGAGGGTTTCACCACTTGTAGAGCTAT
CAGAAGAATGTCAATCAACTGTCCGAGAAAAAAGAATCCCAGG
>Noname
ACTATAAACCCTATTTCTCTTTCTAAAAATTGAAATATTAAAGAAACTAGCACTAGCCTG
ACCTTTAGCCAGACTTCTCACTCTTAATGCTGCGGACAAACAGA
...
I want to... (2 Replies)
Hey,
I've been trying to break a massive fasta formatted file into files containing each gene separately. Could anyone help me? I've tried to use the following code but i've recieved errors every time:
for i in *.rtf.out
do
awk '/^>/{f=++d".fasta"} {print > $i.out}' $i
done (1 Reply)
Hi
I have an alignment file (.fasta) with ~80 sequences. They look like this-
>JV101.contig00066(+):25302-42404|sequence_index=0|block_index=4|species=JV101|JV101_4_0
GAGGTTAATTATCGATAACGTTTAATTAAAGTGTTTAGGTGTCATAATTT
TAAATGACGATTTCTCATTACCATACACCTAAATTATCATCAATCTGAAT... (2 Replies)
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:
>contig0001 length=11115 numreads=10777
agatgtagatctct... (6 Replies)
I have the following script:
awk 'FNR==NR{s+=$3;next;} { print $1 , $2, 100*$3/s }'
and the following file:
>P39PT-1224 Freq 900
cccctacgacggcattggtaatggctcagctgctccggatcccgcaagccatcttggatatgagggttcgtcggcctcttcagccaagg-cccccagcagaacatccagctgatcg
>P39PT-784 Freq 2... (2 Replies)
I have two fasta files as shown below,
File:1
>Contig_1:90600-91187
AAGGCCATCAAGGACGTGGATGAGGTCGTCAAGGGCAAGGAACAGGAATTGATGACGGTC
>Contig_98:35323-35886
GACGAAGCGCTCGCCAAGGCCGAAGAAGAAGGCCTGGATCTGGTCGAAATCCAGCCGCAG
>Contig_24:26615-28387... (11 Replies)
Discussion started by: dineshkumarsrk
11 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)