Splitting fasta AND quality on masked sequence

[mucku]

My scripting skills are the problem... I know some basic shell stuff like grep, sed, awk etc. I come more from the wetlab. Using pre-existing tools and some mild reformatting is ok for me. But I am not sure how to approach this...
I am still trying to learn some biopython in my spare time...

[colindaven]

You can convert to fastQ using a perl script helpfully provided in these forums - I've done this in the past, you'll have to search for it. Then as you say manipulation is easier.

[drio]

I don't think you'll find any tool. Sounds like is time to put your scripting skills to work ?

[mucku]

Hello,
does anybody have a script or any program that allows me to split fasta sequences and the according quality file on masked bases such as "N"? Everything I find works perfectly on fasta files but the quality files are never touched. I think even FastQ format would be ok because conversion is easy these days using Galaxy.

Any help would be appreciated.

Cheers,

Markus

Example:

>fasta
GACTAGCGATCGACGATCGNNNNNNGACGAGCGACGAGCGA
>qual
20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 10 10 10 10 10 10 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20

>fasta_new1
GACTAGCGATCGACGATCG
>fasta_new2
GACGAGCGACGAGCGA
>qual_new1
20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20
>qual_new2
20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20