SeqIO.index does not support gzip files

fhcrc / seqmagick

An imagemagick-like frontend to Biopython SeqIO

http://seqmagick.readthedocs.org

GNU General Public License v3.0

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SeqIO.index does not support gzip files #42

Closed crosenth closed 4 years ago

crosenth commented 10 years ago

http://biopython.org/wiki/SeqIO

We should consider an exit message explaining this issue or write to a temporary file because SeqIO.index (annoyingly) does neither. This affects transform.sort_name and transform.sort_length.

peterjc commented 6 years ago

Its a shame this was never reported to Biopython back in 2014, but it was recently - see https://github.com/biopython/biopython/issues/1666 on giving a better error message.

We could actually index ordinary gzip files (I did this on a branch once), but the performance is terrible - see benchmarks on https://blastedbio.blogspot.co.uk/2011/11/bgzf-blocked-bigger-better-gzip.html

crosenth commented 4 years ago

Thank you Peter for following up on this Issue pointing this out