Can Biopython parse fastq file?

ardmore · 11-29-2011, 10:18 AM

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?

ardmore · 11-29-2011, 02:01 PM

Ignore it. I got it by using pure python.

maubp · 11-29-2011, 02:43 PM

Quote:

Originally Posted by ardmore

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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11-29-2011, 10:18 AM	#1
ardmore Member Location: USA Join Date: Jun 2011 Posts: 51	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?

11-29-2011, 02:01 PM	#2
ardmore Member Location: USA Join Date: Jun 2011 Posts: 51	Ignore it. I got it by using pure python.