Sponsored Content
Top Forums UNIX for Beginners Questions & Answers How to append two fasta files? Post 303035973 by dineshkumarsrk on Tuesday 11th of June 2019 08:44:16 AM
Old 06-11-2019
How to append two files?

I have two fasta files as shown below,
Code:
File:1
>Contig_1:90600-91187 
AAGGCCATCAAGGACGTGGATGAGGTCGTCAAGGGCAAGGAACAGGAATTGATGACGGTC
>Contig_98:35323-35886
GACGAAGCGCTCGCCAAGGCCGAAGAAGAAGGCCTGGATCTGGTCGAAATCCAGCCGCAG               
>Contig_24:26615-28387
GCTGCGGCGCTGATCCTGGCGGCCCGCGCCGAGGAGATCGCCCGTTTGGAGCGCGGCGAA

Code:
File2
>Contig_1:90600-91187
GACCGTCATCAATTCCTGTTCCTTGCCCTTGACGACCTCATCCACGTCCTTGATGGCCTT 
>Contig_24:26615-28387
TTCGCCGCGCTCCAAACGGGCGATCTCCTCGGCGCGGGCCGCCAGGATCAGCGCCG

Both files are having the same fasta headers but vary in terms of sequences. Hence, I need to replace File:2 sequences in File:1 as shown below,
Code:
Expected outcome:
>Contig_1:90600-91187
GACCGTCATCAATTCCTGTTCCTTGCCCTTGACGACCTCATCCACGTCCTTGATGGCCTT 
>Contig_98:35323-35886
GACGAAGCGCTCGCCAAGGCCGAAGAAGAAGGCCTGGATCTGGTCGAAATCCAGCCGCAG
>Contig_24:26615-28387
TTCGCCGCGCTCCAAACGGGCGATCTCCTCGGCGCGGGCCGCCAGGATCAGCGCCG

I tried with
Code:
cat

command, but it is concatenating all the sequences instead of replacing the sequences as I mentioned above.
Please help me to do the same.
Thank you in advance.

Last edited by dineshkumarsrk; 06-13-2019 at 01:36 AM.. Reason: correction
 

10 More Discussions You Might Find Interesting

1. UNIX for Dummies Questions & Answers

append two files

Hi, I have two files where 1 contains data and the other contains strings eg file 1 -0.00000 0.00000 0.00000 0.00000 0.00000 0.80000 0.50000 0.50000 0.60000 0.50000 0.50000 0.20000 -0.00000 0.00000 0.40000 file 2 F F F F F F T T T T T T T T T How to I append file2 to file 1 to... (1 Reply)
Discussion started by: princessotes
1 Replies

2. UNIX for Dummies Questions & Answers

grep FASTA files

I would like to extract the sequences larger than 10 bases but shorter than 18 along with the identifier from a FASTA file that looks like this: > Seq I ACGACTAGACGATAGACGATAGA > Seq 2 ACGATGACGTAGCAGT > Seq 3 ACGATACGAT I know I can extract the IDs alone with the following code grep... (3 Replies)
Discussion started by: Xterra
3 Replies

3. UNIX for Dummies Questions & Answers

renaming (renumbering) fasta files

I have a fasta file that looks like this: >Noname ACCAAAATAATTCATGATATACTCAGATCCATCTGAGGGTTTCACCACTTGTAGAGCTAT CAGAAGAATGTCAATCAACTGTCCGAGAAAAAAGAATCCCAGG >Noname ACTATAAACCCTATTTCTCTTTCTAAAAATTGAAATATTAAAGAAACTAGCACTAGCCTG ACCTTTAGCCAGACTTCTCACTCTTAATGCTGCGGACAAACAGA ... I want to... (2 Replies)
Discussion started by: Oyster
2 Replies

4. Shell Programming and Scripting

append to two files

I tried to write a script ( not working) to append first value from mylist to a file called my myfirstResult and to another called mysecondResult awk ' {print $1} >> myfirsResult ' < mylist awk ' {print $1} >> mysecondResult ' < mylist $ cat mylist A 02/16/2012 B 02/19/2012 C... (3 Replies)
Discussion started by: Sara_84
3 Replies

5. UNIX for Dummies Questions & Answers

Breaking a fasta formatted file into multiple files containing each gene separately

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)
Discussion started by: Ann Mc Cartney
1 Replies

6. UNIX for Dummies Questions & Answers

Append Files

Hi All, I have to append 2 lines at the end of a text file. If those 2 lines are already there then do not append else append the 2 lines to the text file. Eg: I have a text file, file.txt This text file might look like this, /home/kp/make.jsp /home/pk/model.jsp I have to append... (1 Reply)
Discussion started by: pavan_test
1 Replies

7. 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 Replies)
Discussion started by: Mauve
10 Replies

8. Shell Programming and Scripting

Unzip all the files with subdirectories present and append a part of string from the main .zip files

Hi frnds, My requirement is I have a zip file with name say eg: test_ABC_UH_ccde2a_awdeaea_20150422.zip within that there are subdirectories on each directory we again have .zip files and in that we have files like mama20150422.gz and so on. Iam in need of a bash script so that it unzips... (0 Replies)
Discussion started by: Ravi Kishore
0 Replies

9. Shell Programming and Scripting

Append string to all the files inside a directory excluding subdirectories and .zip files

Hii, Could someone help me to append string to the starting of all the filenames inside a directory but it should exclude .zip files and subdirectories. Eg. file1: test1.log file2: test2.log file3 test.zip After running the script file1: string_test1.log file2: string_test2.log file3:... (4 Replies)
Discussion started by: Ravi Kishore
4 Replies

10. Shell Programming and Scripting

Help with reformat single-line multi-fasta into multi-line multi-fasta

Input File: >Seq1 ASDADAFASFASFADGSDGFSDFSDFSDFSDFSDFSDFSDFSDFSDFSDFSD >Seq2 SDASDAQEQWEQeqAdfaasd >Seq3 ASDSALGHIUDFJANCAGPATHLACJHPAUTYNJKG ...... Desired Output File >Seq1 ASDADAFASF ASFADGSDGF SDFSDFSDFS DFSDFSDFSD FSDFSDFSDF SD >Seq2 (4 Replies)
Discussion started by: patrick87
4 Replies
Locale::Script(3perl)					 Perl Programmers Reference Guide				     Locale::Script(3perl)

NAME
Locale::Script - standard codes for script identification SYNOPSIS
use Locale::Script; $script = code2script('phnx'); # 'Phoenician' $code = script2code('Phoenician'); # 'Phnx' $code = script2code('Phoenician', LOCALE_CODE_NUMERIC); # 115 @codes = all_script_codes(); @scripts = all_script_names(); DESCRIPTION
The "Locale::Script" module provides access to standards codes used for identifying scripts, such as those defined in ISO 15924. Most of the routines take an optional additional argument which specifies the code set to use. If not specified, the default ISO 15924 four-letter codes will be used. SUPPORTED CODE SETS
There are several different code sets you can use for identifying scripts. The ones currently supported are: alpha This is a set of four-letter (capitalized) codes from ISO 15924 such as 'Phnx' for Phoenician. This code set is identified with the symbol "LOCALE_SCRIPT_ALPHA". The Zxxx, Zyyy, and Zzzz codes are not used. This is the default code set. numeric This is a set of three-digit numeric codes from ISO 15924 such as 115 for Phoenician. This code set is identified with the symbol "LOCALE_SCRIPT_NUMERIC". ROUTINES
code2script ( CODE [,CODESET] ) script2code ( NAME [,CODESET] ) script_code2code ( CODE ,CODESET ,CODESET2 ) all_script_codes ( [CODESET] ) all_script_names ( [CODESET] ) Locale::Script::rename_script ( CODE ,NEW_NAME [,CODESET] ) Locale::Script::add_script ( CODE ,NAME [,CODESET] ) Locale::Script::delete_script ( CODE [,CODESET] ) Locale::Script::add_script_alias ( NAME ,NEW_NAME ) Locale::Script::delete_script_alias ( NAME ) Locale::Script::rename_script_code ( CODE ,NEW_CODE [,CODESET] ) Locale::Script::add_script_code_alias ( CODE ,NEW_CODE [,CODESET] ) Locale::Script::delete_script_code_alias ( CODE [,CODESET] ) These routines are all documented in the Locale::Codes man page. SEE ALSO
Locale::Codes Locale::Constants http://www.unicode.org/iso15924/ Home page for ISO 15924. AUTHOR
See Locale::Codes for full author history. Currently maintained by Sullivan Beck (sbeck@cpan.org). COPYRIGHT
Copyright (c) 1997-2001 Canon Research Centre Europe (CRE). Copyright (c) 2001-2010 Neil Bowers Copyright (c) 2010-2011 Sullivan Beck This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. perl v5.14.2 2011-09-26 Locale::Script(3perl)
All times are GMT -4. The time now is 12:51 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy