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
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written
by
Eva_Maria
awk '/^>/ {gsub(/.fa(sta)?$/,"",FILENAME);printf(">%s\n",FILENAME);next;} {print}' input.fa
Is there a way to do this for multiple (i.e. several hundred) files at once and output as individual files (with the original names) to a subdirectory? Thanks!
Dear Pierre Lindenbaum. I'm a molecular biologist and I have the same question as theclubstyle "
Is there a way to do this for multiple (i.e. several hundred) files at once and output as individual files (with the original names) to a subdirectory?"
I have read the information on the page shared by you, but I am not able to solve the problem with my limited knowledge in bioinformatics.
I'd appreciate your help.
Assuming all your fasta files are in the current directory and you want to write to outdir
Using a bash loop
for FILE in *.fa;
do
awk '/^>/ {gsub(/.fa(sta)?$/,"",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_{}'
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
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written
by
Ricky •
You mean you want to add the filename to the fasta identifier?
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There is only one record in the file?
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
FILENAMEvariable that you could use for this purpose.