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how split multiple fasta file into multiple file

Hi,

I would like to split multiple fasta file into multiple files where name of each file should be header name without ">" symbol.

For example: 

>contig1
ATACTCTAATTATTA
>contig2
ATACTCTAATTATTA
>contig3
ATACTCTAATTATTA
>contig4
ATACTCTAATTATTA

files should contig1 contig2 contig 3

Number of configs are approximately 20,000.

I found a couple of awk script but it doesn't seem to work. If you feel it is redundant query, I apologize.

Thank you

r sequence rna-seq assembly genome
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updated by ATpoint ATpoint • written by praasu • praasu

2 answers

There you go:

cat test.fa 
>contig1
ATACTCTAATTATTA
>contig2
ATACTCTAATTATTA
>contig3
ATACTCTAATTATTA
>contig4
ATACTCTAATTATTA

## basically as in: https://stackoverflow.com/questions/11818495/split-a-fasta-file-and-rename-on-the-basis-of-first-line
awk '/^>/ {OUT=substr($0,2) ".fa"}; OUT {print >OUT}' test.fa

ls
$ contig1.fa  contig2.fa  contig3.fa  contig4.fa  test.fa
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written by ATpoint ATpoint

foo

• 0 views • link
written by ATpoint ATpoint

Thank you very much for reply

From that link,

First solution doesn't work. It doesn't give any output. awk -F '|' '/^>/ {F=sprintf("%s.fasta",$2); print > F;next;} {print >> F;}' <file name<="" p="">

Second script works but it give file names include (">"). That I don't want. awk -F "|" '/^>/ {close(F) ; F = $1".fasta"} {print >> F}' yourfile.fa

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written by praasu • praasu

Thank you, I used rename command to remove first character from each file,

rename 's/^(.{1})//' *

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written by praasu • praasu

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