how to split multi-fasta file into single fasta file named by header

Question

[Kumar]

I have a multi-fasta file namely genome.fasta as follows

genome.fasta
>LI5896452.1 Liverpool 2 kg/dp/Kng
ATGCTAG
>1582.LC madi kg 5/58/8
GATGAT

I need to split the genome.fasta file into single fasta file and file name should be the corresponding first word of the fasta header. The expected output as follows,

LI5896452.1.fasta
>LI5896452.1 Liverpool 2 kg/dp/Kng
ATGCTAG

1582.LC.fasta
>1582.LC madi kg 5/58/8
GATGAT

I found many script available online but all are splitting the file and naming each by its own, I could not find any script which keeps header as file name. Please help me to do the same.

[GenoMax]

Linearize your fasta file using code here

---

Then use the solutions in: Split Fasta file and rename output files with contig names

[cpad0112]

with awk and flattened fasta:

$ cat test.fa                                                                                                                                                                           
>LI5896452.1 Liverpool 2 kg/dp/Kng
ATGCTAG
>1582.LC madi kg 5/58/8
GATGAT

$ awk -v OFS="\n" '/^>/ {getline seq; print $0,seq > substr($1,2)".fa"}' test.fa  

$ tree .                                                                                                                                                                                
.
├── 1582.LC.fa
├── LI5896452.1.fa
└── test.fa

0 directories, 3 files

$ cat 1582.LC.fa                                                                                                                                                                        
>1582.LC madi kg 5/58/8
GATGAT

$ cat LI5896452.1.fa                                                                                                                                                                    
>LI5896452.1 Liverpool 2 kg/dp/Kng
ATGCTAG

[rsieber]

This only works for the first line of sequences.

Answer 1

[GenoMax]

faSplit utility from Jim Kent (LINK for linux version). Add execute permissions after you download (chmod a+x faSplit).

$ faSplit byname scaffolds.fa outRoot/ 
This breaks up scaffolds.fa using sequence names as file names.
       Use the terminating / on the outRoot to get it to work correctly.

Answer 2

[Jukka Matilainen]

Another solution using AWK:

awk '/^>/ {out = substr($1, 2) ".fasta"; print > out} !/^>/ {print >> out}' genome.fasta

[rsieber]

This is great also for multiline fastas

Answer 3

[shenwei356]

Try seqkit split2

out=result

seqkit split2 --by-size 1 genomes.fasta -O $out

find $out -name "*.fasta" \
    | while read f; do \
        mv $f $out/$(seqkit seq --name --only-id $f).fasta; \
    done

Result

$ tree
.
├── genomes.fasta
└── result
    ├── 1582.LC.fasta
    └── LI5896452.1.fasta

[Kumar]

Thank you shenwei356 , However your script shows error for large dataset as follows,

[INFO] split seqs from genomic.fasta
[INFO] split into 1 seqs per file
[INFO] write 1 sequences to file: result/genomic.part_001.fasta
[INFO] write 1 sequences to file: result/genomic.part_002.fasta
-
-
-
-
-
:line 5:    /bin/ls: Argument list too long

[shenwei356]

Use find instead of ls.

find $out -name "*.fasta" \
    | while read f; do \
        mv $f $out/$(seqkit seq --name --only-id $f).fasta; \
    done

I'm not good at find -exec. You can also use find/fd + parallel

[lieven.sterck]

this means that you created too many files when splitting the original fasta file.

How many entries do you have in your original file? anything above 50-60k entries you will need to subdivide them in subfolders to remain workable.

[azmigueldario]

The following command will give you the fasta files renamed by ID

seqkit split -i [input_fasta] --out-dir [output_directory]

They will be inside the output directory name though you have to rename them as they come with an automatic prefix

[shenwei356]

There's a flag to remove the prefix.

--by-id-prefix ""

Answer 4

[Jorge Amigo]

Quick perl one-liner:

perl -ne 'if (/^>(\S+)/) { close OUT; open OUT, ">$1.fasta" } print OUT' genome.fasta

Answer 5

[Juke34]

In the subject, here a review about how to split fasta file https://github.com/NBISweden/GAAS/blob/master/annotation/knowledge/split_fasta.md Bash and faSplit approach do label fasta file by sequence name, for all other tools it is not mentioned but it does not mean they do not do it.