Command Line tool or library to work with AB1 files

[TaKo]

Hi All.

I have zero experience with sequencing or sequencing files, so please excuse if I ask something stupid

I just learned that colleague of mine needs to regularly do one and the same task - open .ab1 file with Chromas, cut 50 base pairs from the left, save and close it again.
I wonder if there is any way to automate it.
Command line tool, Python/R/java/dotnet library, anything like this.
Any hints?

I tired to google, but found it problematic to use the results I found, so I hope for advise.

Thank you anyway for reading.
Have a good day

[cliffbeall]

There is a EMBOSS program ABIview although that seems to just output fasta format.

Maybe 4peaks with Applescript? Or is there an applescript-like for PC?

[TaKo]

Thanks for reply.

The most discussion in the internet I found talks about converting AB1 to FASTA, looks like it much more common task than editing and saving ab1 itself.

This 4peaks software is it scriptable?

[Gopo]

sangerseqR can parse AB1 files. It doesn't have built in functions to cut 50bp, but you could probably cobble something together with Bioconductor.

http://bioconductor.org/packages/release/bioc/html/sangerseqR.html

[TaKo]

Thanks!
Cutting is not big deal I guess, but unfortunately I do not see any ABIF writing functionality there.

But adding abif instead of abi to my queries I found Bio-Trace-ABIF perl package that also might be usefull