Command Line tool or library to work with AB1 files

TaKo · 02-15-2017, 06:42 AM

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 · 02-15-2017, 07:06 AM

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 · 02-15-2017, 07:24 AM

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 · 02-15-2017, 08:13 AM

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/rel...angerseqR.html

TaKo · 02-15-2017, 08:24 AM

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

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02-15-2017, 06:42 AM	#1
TaKo Junior Member Location: Germany Join Date: Feb 2017 Posts: 3	Command Line tool or library to work with AB1 files 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

02-15-2017, 08:24 AM	#5
TaKo Junior Member Location: Germany Join Date: Feb 2017 Posts: 3	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 Last edited by TaKo; 02-15-2017 at 08:31 AM.

02-15-2017, 07:06 AM	#2
cliffbeall Senior Member Location: Ohio Join Date: Jan 2010 Posts: 144	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?

02-15-2017, 07:24 AM	#3
TaKo Junior Member Location: Germany Join Date: Feb 2017 Posts: 3	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?

02-15-2017, 08:13 AM	#4
Gopo Member Location: Louisiana Join Date: Nov 2013 Posts: 38	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/rel...angerseqR.html