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  • Can Biopython parse fastq file?

    Like so many other Fastq parsers, I made the assumption of a four-line format, but samtools produces a fastq format where sequence and quality runs over multiple lines.
    Can Biopyhton accomodate this format?

  • #2
    Ignore it. I got it by using pure python.

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    • #3
      Originally posted by ardmore View Post
      Like so many other Fastq parsers, I made the assumption of a four-line format, but samtools produces a fastq format where sequence and quality runs over multiple lines.
      Can Biopyhton accomodate this format?
      If you mean Biopython, yes absolutely. See also:
      http://dx.doi.org/10.1093/nar/gkp1137

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