Command or Perl script for changing headers of multiple FASTA files in a specific order listed in a txt file

Question

[adeena_hassan]

Assalam o alaikum everyone,

I am working with multiple genes and in each gene folder i have multiple FASTA (70-75) files and each FASTA file contains single gene sequence. e.g.

AMY2b_Gene_folder

Chimpanzee_AMY2B_CDS.fasta
Human_AMY2B_CDS.fasta
Pygmy_chimpanzee_AMY2B_CDS.fasta
Western_gorrila_AMY2B_CDS.fasta

cat Chimpanzee_AMY2B_CDS.fasta

>lcl|NM_020978.4_cds_NP_066188.1_1 [gene=AMY2B] [protein=alpha-amylase 2B precursor] [protein_id=NP_066188.1] [location=673..2208]
ATGAAGTTCTTTCTGTTGCTTTTCACCATTGGGTTCTGCTGGGCTCAGTATTCCCCAAATACACAACAAG
GACGGACATCTATTGTTCATCTGTTTGAATGGCGATGGGTTGATATTGCTCTTGAATGTGAGCGATATTT
AGCTCCCAAGGGATTTGGAGGGGTTCAGGTCTCTCCACCAAATGAAAATGTTGCAATTCACAACCCTTTC

Human_AMY2B_CDS.fasta

 >lcl|NM_020978.4_cds_NP_066188.1_1 [gene=AMY2B] [protein=alpha-amylase 2B precursor] [protein_id=NP_066188.1] [location=673..2208]
> ATGAAGTTCTTTCTGTTGCTTTTCACCATTGGGTTCTGCTGGGCTCAGTATTCCCCAAATACACAACAAG
> GACGGACATCTATTGTTCATCTGTTTGAATGGCGATGGGTTGATATTGCTCTTGAATGTGAGCGATATTT
> AGCTCCCAAGGGATTTGGAGGGGTTCAGGTCTCTCCACCAAATGAAAATGTTGCAATTCACAACCCTTTC

I want to change headers of each fasta file according to a specific order given in text file.

cat Headers.txt
MP.C_AMY2B
FP.H_AMY2B

The output should be look like

>MP.C_AMY2B
 ATGAAGTTCTTTCTGTTGCTTTTCACCATTGGGTTCTGCTGGGCTCAGTATTCCCCAAATACACAACAAG GACGGACATCTATTGTTCATCTGTTTGAATGGCGATGGGTTGATATTGCTCTTGAATGTGAGCGATATTT AGCTCCCAAGGGATTTGGAGGGGTTCAGGTCTCTCCACCAAATGAAAATGTTGCAATTCACAACCCTTTC

I have tried perl script given in following biostar posts but these scripts did not worked for multiple FASTA files which have single gene sequence.

Renaming Entries In A Fasta File

Renaming fasta headers according to a matching name list

Kindly guide me is there any command-line solution to do so????

[shenwei356]

Without the mapping rule of names in Headers.txt and the FASTA files, we can't rename them rightly.

Chimpanzee_AMY2B_CDS.fasta                 MP.C_AMY2B
Human_AMY2B_CDS.fasta                      FP.H_AMY2B
Pygmy_chimpanzee_AMY2B_CDS.fasta           ????
Western_gorrila_AMY2B_CDS.fasta            ?????

Answer 1

[cpad0112]

Run this command:

$ for i in $(sed -n '=' headers.txt); do sed -n "$i"p headers.txt| sed 's/^/>/'; cat $(ls *.fasta| sed -n "$i"p)| sed '1d'; done

output:

>MP.C_AMY2B
ATGAAGTTCTTTCTGTTGCTTTTCACCATTGGGTTCTGCTGGGCTCAGTATTCCCCAAATACACAACAAG
GACGGACATCTATTGTTCATCTGTTTGAATGGCGATGGGTTGATATTGCTCTTGAATGTGAGCGATATTT
AGCTCCCAAGGGATTTGGAGGGGTTCAGGTCTCTCCACCAAATGAAAATGTTGCAATTCACAACCCTTTC
>FP.H_AMY2B
ATGAAGTTCTTTCTGTTGCTTTTCACCATTGGGTTCTGCTGGGCTCAGTATTCCCCAAATACACAACAAG
GACGGACATCTATTGTTCATCTGTTTGAATGGCGATGGGTTGATATTGCTCTTGAATGTGAGCGATATTT
AGCTCCCAAGGGATTTGGAGGGGTTCAGGTCTCTCCACCAAATGAAAATGTTGCAATTCACAACCCTTTC

Assumptions

1. Order fasta sequences are in the same order as the headers to be replaced in headers.txt
2. User default shell is bash

Note: Output to the screen. You can redirect to another fasta file.

Input:

$ cat headers.txt 
MP.C_AMY2B
FP.H_AMY2B

$ cat *.fasta
>lcl|NM_020978.4_cds_NP_066188.1_1 [gene=AMY2B] [protein=alpha-amylase 2B precursor] [protein_id=NP_066188.1] [location=673..2208]
ATGAAGTTCTTTCTGTTGCTTTTCACCATTGGGTTCTGCTGGGCTCAGTATTCCCCAAATACACAACAAG
GACGGACATCTATTGTTCATCTGTTTGAATGGCGATGGGTTGATATTGCTCTTGAATGTGAGCGATATTT
AGCTCCCAAGGGATTTGGAGGGGTTCAGGTCTCTCCACCAAATGAAAATGTTGCAATTCACAACCCTTTC
>lcl|NM_020978.4_cds_NP_066188.1_1 [gene=AMY2B] [protein=alpha-amylase 2B precursor] [protein_id=NP_066188.1] [location=673..2208]
ATGAAGTTCTTTCTGTTGCTTTTCACCATTGGGTTCTGCTGGGCTCAGTATTCCCCAAATACACAACAAG
GACGGACATCTATTGTTCATCTGTTTGAATGGCGATGGGTTGATATTGCTCTTGAATGTGAGCGATATTT
AGCTCCCAAGGGATTTGGAGGGGTTCAGGTCTCTCCACCAAATGAAAATGTTGCAATTCACAACCCTTTC

[adeena_hassan]

Thank u so much, your solution is useful. i want to redirect output in the multiple input fasta files.

[cpad0112]

create a folder called test (in the same folder where fasta files are located) and run the command:

$ mkdir test

execute:

for i in $(seq 1 $(ls *.fasta |wc -l)); do sed -n "$i"p headers.txt| sed 's/^/>/'> test/$(ls *.fasta| sed -n "$i"p); cat $(ls *.fasta| sed -n "$i"p)| sed '1d' >>test/$(ls *.fasta| sed -n "$i"p); done

files in test folder will have exact names as fasta files in current directory. Let me know if there are any issues with the script.

[adeena_hassan]

Thank u so much it's working.. You made my day :)

Answer 2

[tiago211287]

First, create a backup of all files before trying this approach.

Taking a list of new headers, namely, Headers.txt

cat Headers.txt
MP.C_AMY2B
FP.H_AMY2B

in the same order of one fasta files list

find . -maxdepth 1 -name "*CDS.fasta" | sort
./Chimpanzee_AMY2B_CDS.fasta
./Human_AMY2B_CDS.fasta

put the following function in your linux enviroment:

function sedinho () { sed -i  "s/^.*\]/>$1/g" $2;}
export -f sedinho

create variables of : list of new headers (LIST1) list of input files (LIST2)

LIST1=($(cat Headers.txt))
LIST2=($(find /folder/with/fasta/files/ -maxdepth 0 -name "*CDS.fasta" | sort))

parallel --xapply sedinho {1} {2} ::: ${LIST1[@]} ::: ${LIST2[@]}


>MP.C_AMY2B
ATGAAGTTCTTTCTGTTGCTTTTCACCATTGGGTTCTGCTGGGCTCAGTATTCCCCAAATACACAACAAG
GACGGACATCTATTGTTCATCTGTTTGAATGGCGATGGGTTGATATTGCTCTTGAATGTGAGCGATATTT
AGCTCCCAAGGGATTTGGAGGGGTTCAGGTCTCTCCACCAAATGAAAATGTTGCAATTCACAACCCTTTC

[adeena_hassan]

Hi tiago211287 , Thank you for your reply. I have tried your solution but the following error occurred.

zsh:1: command not found: sedinho
zsh:1: command not found: sedinho
zsh:1: command not found: sedinho

for putting function in my linux environment i have simply copied function in a text file and copied the file in bin folder. but the above error occurred again can you tell me how to fix it ????

[tiago211287]

in order to work you must execute this two lines in your terminal:

function sedinho () { sed -i  "s/^.*\]/>$1/g" $2;}
export -f sedinho

you dont need to put this inside a file

[adeena_hassan]

yup,, Firstly i executed above lines in my terminal but same error occurred. :(

[tiago211287]

can you repeat what you're doing and post a screenshot of your screen here?

[adeena_hassan]

https://ibb.co/bz2ita![enter image description here][1]

https://ibb.co/dd3v6v![enter image description here][2]

https://ibb.co/e8tnmv

[GenoMax]

You can't directly attach files to Biostars posts. Use a free image hosting provider (click on the icon next to "101" one in edit window to get some suggestions) to upload your images and then insert those links here.

[tiago211287]

this is strange to me, it appears that your shell is not exporting the function properly

[GenoMax]

This user appears to be using zsh and that may be the difference. Switching to bash may do the trick.

Answer 3

[biolab]

Please check the following commnds. First, run cd AMY2b_Gene_folder/; mkdir new/. Then, run for f in *.fasta; do perl -e '$in=$ARGV[0]=~s/(.+?)\.fasta/$1/r; while (<>){if (/>/) {print ">$in\n"} else {print} }' $f > new/$f; done

[adeena_hassan]

Hi biolab,

Thank you for your reply. But i have new FASTA headers in a separate text file according to fasta files oder above code replace headers with FASTA file name not with the headers in the headers file. can u guide me where to use headers file???

P.S I'm new in bioinformatics world happy to give more information.