Linux question

[Saeideh]

I have a complete genome sequence fasta file. (seq.fasta)

Like this (but tens of lines):

AAGGGGCGGCGGCGGGGTTTGTTT
TTTTGGGGCGGGCTTGAGGAGGGG
CCGGTTAGGGACCGTTGGCCGGGC
...

I want to make it like this:

read1
AAGGGGCGGCGGCGGGGTTTGTTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFF
read2
TTTTGGGGCGGGCTTGAGGAGGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFF

how can I do that in Ubuntu terminal?

[Michael.Ante]

Hi Saeideh,

awk would be my program of choice:

awk '{printf "read%d\n%s\n+\nFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n",NR,$1}' seq.fasta > seq.fastq

This will only work if the sequences have all the same length; otherwise you need to adept the length of the quality string.
Maybe reformat.sh from bbmap could also do the job.

[Saeideh]

Done~

It worked for meeee. Thank you Michaeeeeeeeeeeeel ~~~

[maubp]

What are you doing? It looks almost like FASTQ output with dummy quality scores of F, but missing the @ marker.