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  • existing tool to extract sequence ranges from multifasta file

    I can't believe there's been no solution for this problem in 2016, but I seem to be incapable to find it.

    Does anyone of you know some tool that is able to extract multiple sequence ranges from a regular multifasta file based on sequence accession and range?

    For example, given a file with three accessions like

    >scaf_1315 dna:supercontig supercontig:GCA_000156735.1:scaf_1315:1:42565:1
    >scaf_1316 dna:supercontig supercontig:GCA_000156735.1:scaf_1316:1:70442:1
    >scaf_1311 dna:supercontig supercontig:GCA_000156735.1:scaf_1311:1:1389502:1


    I'd like extract range 500-600 from scaf_1315, 2000-4500 from scaf_1316 and nothing from scaf_1311.

    I'd love to find something stable and as easy to use like seqret or extractseq from the EMBOSS packages, but either I have to split the input fasta into one sequence per file (extractseq) or I get the same range from all accessions (seqret) and have to filter the output again.

    I'm perfectly able to code something like this in a custom script (this is what I'll do now anyway), but I feel like I missing something as obvious as an EMBOSS package.

  • #2
    You don't need to code this yourself. Use samtools faidx or pyfaidx.

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    • #3
      @GenoMax, awesome thank you so much. This is exactly what I was looking for, despite using samtools frequently for anything sam/bam related, I completely ignored its fasta options.
      EDIT: the bioperl solution in the same quoted thread proofed to be even easier for me in this particular case
      Last edited by CarambaKaracho; 06-30-2016, 06:32 AM. Reason: Additional comment

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