I have a fastq file from small RNA sequencing with sequence lengths between 15 - 30. I wanted to filter sequence lengths between 21-25 and write to another fastq file. how can i do that? (4 Replies)
Hi,
I am having a file of dna sequences in fasta format which look like this:
>admin_1_45
atatagcaga
>admin_1_46
atatagcagaatatatat
with many such thousands of sequences in a single file. I want to the replace the accession Id "admin_1_45" similarly in following sequences to... (5 Replies)
I have two files. File1 is shown below.
>153L:B|PDBID|CHAIN|SEQUENCE
RTDCYGNVNRIDTTGASCKTAKPEGLSYCGVSASKKIAERDLQAMDRYKTIIKKVGEKLCVEPAVIAGIISRESHAGKVL
KNGWGDRGNGFGLMQVDKRSHKPQGTWNGEVHITQGTTILINFIKTIQKKFPSWTKDQQLKGGISAYNAGAGNVRSYARM
DIGTTHDDYANDVVARAQYYKQHGY
>16VP:A|PDBID|CHAIN|SEQUENCE... (7 Replies)
Hello,
I have 10 fasta files with sequenced reads information with read sizes from 15 - 35 . I have combined the reads and collapsed in to unique reads and filtered for sizes 18 - 26 bp long unique reads. Now i wanted to count each unique read appearance in all the fasta files and make a table... (5 Replies)
I have a fasta file as follows
>sp|O15090|FABP4_HUMAN Fatty acid-binding protein, adipocyte OS=Homo sapiens GN=FABP4 PE=1 SV=3
MCDAFVGTWKLVSSENFDDYMKEVGVGFATRKVAGMAKPNMIISVNGDVITIKSESTFKN
TEISFILGQEFDEVTADDRKVKSTITLDGGVLVHVQKWDGKSTTIKRKREDDKLVVECVM
KGVTSTRVYERA
>sp|L18484|AP2A2_RAT AP-2... (3 Replies)
Hi
How can I extract sequences from a fasta file with respect a certain criteria? The beginning of my file (containing in total more than 1000 sequences) looks like this:
>H8V34IS02I59VP
SDACNDLTIALLQIAREVRVCNPTFSFRWHPQVKDEVMRECFDCIRQGLG
YPSMRNDPILIANCMNWHGHPLEEARQWVHQACMSPCPSTKHGFQPFRMA... (6 Replies)
Hi,
I have a fasta file with multiple sequences. How can i get only unique sequences from the file.
For example
my_file.fasta
>seq1
TCTCAAAGAAAGCTGTGCTGCATACTGTACAAAACTTTGTCTGGAGAGATGGAGAATCTCATTGACTTTACAGGTGTGGACGGTCTTCAGAGATGGCTCAAGCTAACATTCCCTGACACACCTATAGGGAAAGAGCTAAC
>seq2... (3 Replies)
I have this file:
>ID1
AA
>ID2
TTTTTT
>ID-3
AAAAAAAAA
>ID4
TTTTTTGGAGATCAGTAGCAGATGACAG-GGGGG-TGCACCCC
Add I am trying to use this script to output sequences longer than 15 characters:
sed -r '/^>/N;{/^.{,15}$/d}'
The desire output would be this:
>ID4... (8 Replies)
I have a fasta file as follows
>sp|Q8WWQ8|STAB2_HUMAN Stabilin-2 OS=Homo sapiens OX=9606 GN=STAB2 PE=1 SV=3
MMLQHLVIFCLGLVVQNFCSPAETTGQARRCDRKSLLTIRTECRSCALNLGVKCPDGYTM
ITSGSVGVRDCRYTFEVRTYSLSLPGCRHICRKDYLQPRCCPGRWGPDCIECPGGAGSPC
NGRGSCAEGMEGNGTCSCQEGFGGTACETCADDNLFGPSCSSVCNCVHGVCNSGLDGDGT... (3 Replies)
Hi,
I have to add 7 bases of specific nucleotide at the beginning and ending of all the fasta sequences of a file. For example, I have a multi fasta file namely test.fasta as given below
test.fasta
>TalAA18_Xoo_CIAT_NZ_CP033194.1:_2936369-2939570:+1... (1 Reply)
Discussion started by: dineshkumarsrk
1 Replies
LEARN ABOUT MOJAVE
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) 2011-2013 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 2013-11-04 Locale::Codes::LangFam(3pm)
04-09-2019
