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Old 11-29-2011, 11:18 AM   #1
ardmore
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Default 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?
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Old 11-29-2011, 03:01 PM   #2
ardmore
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Ignore it. I got it by using pure python.
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Old 11-29-2011, 03:43 PM   #3
maubp
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Quote:
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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