Change header of a Fasta file according to the file name

Question

[Eva_Maria]

Hai

I have a Fasta file like GCA_001609185.1_ASM160918v1_genomic.fsa and i want to change header of this fasta file like this >GCA_001609185.1_ASM160918v1_genomic
I am looking for solutions

Thank you

[WouterDeCoster]

There is only one record in the file?

[Devon Ryan]

This is kind of off topic, so I won't be overly surprised if someone closes it. Having said that, note that awk has a FILENAME variable that you could use for this purpose.

Answer 1

[Pierre Lindenbaum]

 awk '/^>/ {gsub(/.fa(sta)?$/,"",FILENAME);printf(">%s\n",FILENAME);next;} {print}' input.fa

[theclubstyle]

Is there a way to do this for multiple (i.e. several hundred) files at once and output as individual files (with the original names) to a subdirectory? Thanks!

[Pierre Lindenbaum]

http://tldp.org/HOWTO/Bash-Prog-Intro-HOWTO-7.html

[Gonzalo]

Dear Pierre Lindenbaum. I'm a molecular biologist and I have the same question as theclubstyle "

Is there a way to do this for multiple (i.e. several hundred) files at once and output as individual files (with the original names) to a subdirectory?"

I have read the information on the page shared by you, but I am not able to solve the problem with my limited knowledge in bioinformatics.

I'd appreciate your help.

[WouterDeCoster]

Assuming all your fasta files are in the current directory and you want to write to outdir

Using a bash loop

for FILE in *.fa;
do
 awk '/^>/ {gsub(/.fa(sta)?$/,"",FILENAME);printf(">%s\n",FILENAME);next;} {print}' $FILE > outdir/changed_${FILE}
done

Using GNU parallel

ls *.fa | parallel 'awk '/^>/ {gsub(/.fa(sta)?$/,"",FILENAME);printf(">%s\n",FILENAME);next;} {print}' {} > outdir/changed_{}'

[Gonzalo]

It works! :) . Deeply grateful for your help,

Regards

[Ricky]

Hi @WouterDeCoster, This command script is helpful. Thank you. Would you please help me make a script if we want to keep the sentence and add the file name together?

for example, my file name is HP1 and HP2.

HP1 is this:

>NODE_1_length_179136_cov_279.866497
>NODE_2_length_175370_cov_263.866948

HP2 is this:

>NODE_1_length_134626_cov_266.846339
>NODE_2_length_107967_cov_280.028186

I want to change become:

HP1 becomes:

>HP1 NODE_1_length_179136_cov_279.866497

>HP1 NODE_2_length_175370_cov_263.866948

HP2 becomes:

>HP2 NODE_1_length_134626_cov_266.846339

>HP2 NODE_2_length_107967_cov_280.028186

or in the second condition, if possible, become:

HP1 becomes:

>HP1 1

>HP1 2

HP2 becomes:

>HP2 1

>HP2 2

Thank you so much

[cpad0112]

please post this as a new post with the details and link to this post. @ Ricky

[WouterDeCoster]

You mean you want to add the filename to the fasta identifier?