Question

Biopython And Fastqgeneraliterator

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11.7 years ago

nupurgupta0806 ▴ 30

I am trying FastqGeneralIterator. Which is pretty fast, faster that the SeqIO.parse I was using. The only problem is that - say for an original record

@M12MX:9:47
AGTCTATAC
+
0::99:DDD

It removes the @ from the 1st line, and does not have information for the 3rd line. I could just put them in, but I would be guessing. Does anyone have a solution for this?

Thanks

biopython fastq • 2.7k views

ADD COMMENT • link 11.7 years ago by nupurgupta0806 ▴ 30

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Thanks very much

ADD REPLY • link 11.7 years ago by nupurgupta0806 ▴ 30

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You should add comments like this by clicking the comment hyperlink under brentp's answer.

ADD REPLY • link 11.7 years ago by Steve Moss 2.3k

score 2 · Accepted Answer · 2012-08-28

You can read the code to see what it is doing: https://github.com/biopython/biopython/blob/master/Bio/SeqIO/QualityIO.py#L785

It only removes the "@" after checking that's the first character of the title line.

For the 2nd title line, it checks that it starts with "+". If there are more characters, it checks that it matches the title line. So, if your file does have info in the 3rd line, it has to be redundant or FastqGeneralIterator would generate an error.

You don't have to guess about the first line, just add the "@" back in.