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????
•
written
by
adeena_hassan •
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
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
Thank u so much, your solution is useful. i want to redirect output in the multiple input fasta files.
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.
Thank u so much it's working.. You made my day :)
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
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 ????
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
yup,, Firstly i executed above lines in my terminal but same error occurred. :(
can you repeat what you're doing and post a screenshot of your screen here?
https://ibb.co/bz2ita![enter image description here][1]
https://ibb.co/dd3v6v![enter image description here][2]
this is strange to me, it appears that your shell is not exporting the function properly
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.
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Without the mapping rule of names in Headers.txt and the FASTA files, we can't rename them rightly.