change headers from fasta files

Question

[ulises.rodriguez]

I have multifasta files containing sequences like these:

>16S_ribosomal_RNA
attgcaggtcagcatactgcagtgaattcgttcc

>16S_ribosomal_RNA
attgcaggtcagcatactgcagtgaattcgttcc

>16S_ribosomal_RNA
attgcaggtcagcatactgcagtgaattcgttcc

these sequences are contained in fasta files named as following :

Bacteria_especie_strain.fasta

and I would like that headers has the same name that the multifasta file :

>16S_ribosomal_RNA_Bacteria_especie_strain.fasta 
attgcaggtcagcatactgcagtgaattcgttcc

> 16S_ribosomal_RNA_Bacteria_especie_strain.fasta 
attgcaggtcagcatactgcagtgaattcgttcc

>16S_ribosomal_RNA_Bacteria_especie_strain.fasta 
attgcaggtcagcatactgcagtgaattcgttcc

Answer 1

[cschu181]

awk -v fn="Bacteria_especie_strain.fasta"  '/^>/ { print $0"_"fn; next; } { print $0; }' Bacteria_especie_strain.fasta > Bacteria_especie_strain.fasta.modified_headers

Answer 2

[h.mon]

See answers from Question: Changing names of Fasta headers.

Answer 3

[cpad0112]

Output from awk:

 $ awk   '/^>/ { print $0"_"FILENAME; next}1' Bacteria_especie_strain.fasta

>16S_ribosomal_RNA_Bacteria_especie_strain.fasta
attgcaggtcagcatactgcagtgaattcgttcc
>16S_ribosomal_RNA_Bacteria_especie_strain.fasta
attgcaggtcagcatactgcagtgaattcgttcc
>16S_ribosomal_RNA_Bacteria_especie_strain.fasta
attgcaggtcagcatactgcagtgaattcgttcc

output from sed and parallel:

$ parallel  'sed "/^>/ s/.*/&_{}/g"' {} ::: Bacteria_especie_strain.fasta 

>16S_ribosomal_RNA_Bacteria_especie_strain.fasta
attgcaggtcagcatactgcagtgaattcgttcc
>16S_ribosomal_RNA_Bacteria_especie_strain.fasta
attgcaggtcagcatactgcagtgaattcgttcc
>16S_ribosomal_RNA_Bacteria_especie_strain.fasta
attgcaggtcagcatactgcagtgaattcgttcc

input:

$ cat Bacteria_especie_strain.fasta 

>16S_ribosomal_RNA
attgcaggtcagcatactgcagtgaattcgttcc
>16S_ribosomal_RNA
attgcaggtcagcatactgcagtgaattcgttcc
>16S_ribosomal_RNA
attgcaggtcagcatactgcagtgaattcgttcc