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  • 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

  • #2
    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?

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    • #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?

      Comment


      • #4
        sangerseqR can parse AB1 files. It doesn't have built in functions to cut 50bp, but you could probably cobble something together with Bioconductor.
        This package contains several tools for analyzing Sanger Sequencing data files in R, including reading .scf and .ab1 files, making basecalls and plotting chromatograms.

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        • #5
          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, 09:31 AM.

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