[Biopython-dev] [Biopython] SeqIO.index improvement suggestions

Peter biopython at maubp.freeserve.co.uk
Wed Feb 24 17:03:09 UTC 2010


Hi all,

I've updated my branch to cope with gzipped FASTQ files, tested on
Windows XP, Mac OS X Snow Leopard, and Linux:

http://github.com/peterjc/biopython/tree/index-zip

This works by just opening gzipped files in default mode - which
seems to be fine with the examples (FASTA, QUAL and FASTQ)
where the text file in the archive uses Unix new line entries.

While this may be a good solution, we should test on gzipped
files containing Windows new lines too. Plus of course, try
non-gzipped compression. And very large files. etc.

Peter



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