Formatting Reads to fasta

Question

[Gabe Anderson]

Hi,

I have a file with reads and read counts like this:

CGTAGTTGAACTTGTGCTTCAT  8
ATCCCCGGCATCTCCGCCA 1
TGAGAATAGTGTGCATTT 52

I'd appreciate some help converting it to look like this:

>dme_1_count=8
CGTAGTTGAACTTGTGCTTCAT
>dme_2_count=1
ATCCCCGGCATCTCCGCCA
>dme_3_count=52
TGAGAATAGTGTGCATTT

count = number at the end of each read dme_x, x = unique number.

I also want to delete reads with count<=2. However, I want the processes separate.

Thank you!

[venu]

You can modify this answer according to your task.

Answer 1

[JC]

perl -lane ' print ">dme_" . $n++ . "_count=$F[1]\n$F[0]" if ($F[1] > 2) ' < table > fasta

[Gabe Anderson]

Thank you! It worked perfectly

Answer 2

[gangireddy]

awk '($2 >2) {print ">dme_"NR"count="$2"\n"$1"\n"}' table > output.fasta

[Gabe Anderson]

Thanks a lot! The code works