convert unique tags to fasta

Question

[manishbiotechie]

I have a large fasta file of microRNA where unique tag is there in form of

>sequence1_x5
AGCTAGCTAGCTAGCT
>sequence2_x15
ATCTATCTATCT

and i want to convert into individual fasta file as

>1
AGCTAGCTAGCTAGCT
>2
AGCTAGCTAGCTAGCT
>3
AGCTAGCTAGCTAGCT
>4
AGCTAGCTAGCTAGCT
>5
AGCTAGCTAGCTAGCT
>6
ATCTATCTATCT
>7
ATCTATCTATCT

and so on....

I am new to bioinformatics kindly help

[manishbiotechie]

its not taking the right format i have asked question in fasta format but some error is there while posting

[GenoMax]

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Thank you!

[GenoMax]

See the first answer in this thread: Renaming Entries In A Fasta File

 awk '/^>/{print ">" ++i; next}{print}' < file.fasta > new.fasta

[AK]

This returns:

>1
AGCTAGCTAGCTAGCT
>2
ATCTATCTATCT

Without considering x5 and x15.

[GenoMax]

Indeed. Left here as an inspiration. Useful for anyone else who may find this thread by search.

Answer 1

[AK]

Hi manishbiotechie,

You can try:

$ cat input.fasta
>sequence1_x5
AGCTAGCTAGCTAGCT
>sequence2_x15
ATCTATCTATCT

$ cat input.fasta | awk 'BEGIN{RS=">"; i=1} NR>1 {gsub(".+_x", "", $1); {while ($1--) {print ">" i "\n" $2; i++}}}'
>1
AGCTAGCTAGCTAGCT
>2
AGCTAGCTAGCTAGCT
>3
AGCTAGCTAGCTAGCT
>4
AGCTAGCTAGCTAGCT
>5
AGCTAGCTAGCTAGCT
>6
ATCTATCTATCT
>7
ATCTATCTATCT
>8
ATCTATCTATCT
>9
ATCTATCTATCT
>10
ATCTATCTATCT
>11
ATCTATCTATCT
>12
ATCTATCTATCT
>13
ATCTATCTATCT
>14
ATCTATCTATCT
>15
ATCTATCTATCT
>16
ATCTATCTATCT
>17
ATCTATCTATCT
>18
ATCTATCTATCT
>19
ATCTATCTATCT
>20
ATCTATCTATCT