Sponsored Content
Top Forums UNIX for Beginners Questions & Answers How to append two fasta files? Post 303035982 by vgersh99 on Tuesday 11th of June 2019 12:05:52 PM
Old 06-11-2019
not sure if I follow your samples and the desired output, but I think you might want this.

awk -f dinesh.awk file2 file1 where dinesh.awk is:
Code:
FNR==NR {
  if (FNR%2)
     head=$0
  else
     f2[head]=$0
  next
}
{
  if (FNR%2) {
     head=$0
     print
  }
  else
     print (head in f2)? f2[head] : $0
}

results in:
Code:
>Contig_1:90600-91187
GACCGTCATCAATTCCTGTTCCTTGCCCTTGACGACCTCATCCACGTCCTTGATGGCCTT
>Contig_98:35323-35886
GACGAAGCGCTCGCCAAGGCCGAAGAAGAAGGCCTGGATCTGGTCGAAATCCAGCCGCAG
>Contig_24:26615-28387
TTCGCCGCGCTCCAAACGGGCGATCTCCTCGGCGCGGGCCGCCAGGATCAGCGCCG


Last edited by vgersh99; 06-11-2019 at 01:37 PM..
These 3 Users Gave Thanks to vgersh99 For This Post:
 

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
GIT-CHERRY(1)							    Git Manual							     GIT-CHERRY(1)

NAME
git-cherry - Find commits not merged upstream SYNOPSIS
git cherry [-v] [<upstream> [<head> [<limit>]]] DESCRIPTION
The changeset (or "diff") of each commit between the fork-point and <head> is compared against each commit between the fork-point and <upstream>. The commits are compared with their patch id, obtained from the git patch-id program. Every commit that doesn't exist in the <upstream> branch has its id (sha1) reported, prefixed by a symbol. The ones that have equivalent change already in the <upstream> branch are prefixed with a minus (-) sign, and those that only exist in the <head> branch are prefixed with a plus (+) symbol: __*__*__*__*__> <upstream> / fork-point \__+__+__-__+__+__-__+__> <head> If a <limit> has been given then the commits along the <head> branch up to and including <limit> are not reported: __*__*__*__*__> <upstream> / fork-point \__*__*__<limit>__-__+__> <head> Because git cherry compares the changeset rather than the commit id (sha1), you can use git cherry to find out if a commit you made locally has been applied <upstream> under a different commit id. For example, this will happen if you're feeding patches <upstream> via email rather than pushing or pulling commits directly. OPTIONS
-v Verbose. <upstream> Upstream branch to compare against. Defaults to the first tracked remote branch, if available. <head> Working branch; defaults to HEAD. <limit> Do not report commits up to (and including) limit. SEE ALSO
git-patch-id(1) GIT
Part of the git(1) suite Git 1.7.10.4 11/24/2012 GIT-CHERRY(1)
All times are GMT -4. The time now is 10:09 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy