Sponsored Content
Top Forums UNIX for Beginners Questions & Answers How to append two fasta files? Post 303036069 by Scrutinizer on Thursday 13th of June 2019 12:30:46 PM
Old 06-13-2019
awk version you could try:
Code:
awk 'BEGIN{FS=RS; RS=">"; ORS=""} FNR>1{A[$1]=RS $0} END{for(i in A) print A[i]}'  file1 file2

note: ensure that there are no excess trailing spaces as is the case with the file samples.

Last edited by Scrutinizer; 06-13-2019 at 01:50 PM..
These 3 Users Gave Thanks to Scrutinizer 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
JOIN(1) 						      General Commands Manual							   JOIN(1)

NAME
join - relational database operator SYNOPSIS
join [ options ] file1 file2 DESCRIPTION
Join forms, on the standard output, a join of the two relations specified by the lines of file1 and file2. If file1 is `-', the standard input is used. File1 and file2 must be sorted in increasing ASCII collating sequence on the fields on which they are to be joined, normally the first in each line. There is one line in the output for each pair of lines in file1 and file2 that have identical join fields. The output line normally con- sists of the common field, then the rest of the line from file1, then the rest of the line from file2. Fields are normally separated by blank, tab or newline. In this case, multiple separators count as one, and leading separators are dis- carded. These options are recognized: -an In addition to the normal output, produce a line for each unpairable line in file n, where n is 1 or 2. -e s Replace empty output fields by string s. -jn m Join on the mth field of file n. If n is missing, use the mth field in each file. -o list Each output line comprises the fields specified in list, each element of which has the form n.m, where n is a file number and m is a field number. -tc Use character c as a separator (tab character). Every appearance of c in a line is significant. SEE ALSO
sort(1), comm(1), awk(1) BUGS
With default field separation, the collating sequence is that of sort -b; with -t, the sequence is that of a plain sort. The conventions of join, sort, comm, uniq, look and awk(1) are wildly incongruous. 7th Edition April 29, 1985 JOIN(1)
All times are GMT -4. The time now is 06:29 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy