converting scf to ab1/abi

[PedroDaPos]

Hi! I am using Staden/io_lib via a conda installation to convert scf files to ab1/abi (the context here is that there is a R package I am using for trace analysis, for a reproducible example, but it only accepts ab1 files). I am running the following command:

convert_trace scf ab1 < input_file.scf > output_file.ab1

Everything seems to work fine, but when I try to use this file neither the R package or even Geneious recognizes this file as ab1 format. I was wondering if you would be able to give me some advice on what I might be doing wrong. Thank you in advance for your help!

[jkbonfield]

Hello, Sorry for the slow reply.

On Fri, Dec 15, 2023 at 12:39:45PM -0800, PedroDaPos wrote: Hi! I am using Staden/io_lib via a conda installation to convert scf files to ab1/abi (the context here is that there is a R package I am using for trace analysis, for a reproducible example, but it only accepts ab1 files). I am running the following command: convert_trace scf ab1 < input_file.scf > output_file.ab1 Everything seems to work fine, but when I try to use this file neither the R package or even Geneious recognizes this file as ab1 format. I was wondering if you would be able to give me some advice on what I might be doing wrong. Thank you in advance for your help!

It's been decades since I worked on that code! Everything involving AB1 was reverse engineered by various groups because ABI wanted to keep it top secret and lock people into their format. While the basic structure is well known, it's a tagged key-value pair format and there are a lot of extra ancillary fields which may or may not be needed by various tools. Io_lib never implemented AB1 writing. Only reading. This was deliberate as we didn't want to promote secrecy and use of proprietary file formats. It's a bug though that the tool didn't give an error on usage. No doubt it wrote out ZTR instead. Try doing "less output_file.ab1" and you'll see the header bytes. I think you'd be better off speaking to the authors of the R package and requesting that they support one of the public file formats instead. (I see Geneious supports SCF) James

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-- James Bonfield ***@***.***) The Sanger Institute, Hinxton, Cambs, CB10 1SA

-- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA.

[PedroDaPos]

Thank you for clarifying this, I really appreciated it! I reached out to the R package authors. Have a nice new year!