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arq5x / poretools

a toolkit for working with Oxford nanopore data
MIT License
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new ISO format for exp_start_time written by minKNOW #119

Closed sengelen closed 7 years ago

sengelen commented 7 years ago

Hi everyone,

The format of exp_start_time has changed. It is now in ISO format, so poretools throw an error when trying to convert it in int. I think a test and a date conversion in function get_exp_start_time() of Fast5File.py should resolve this issue.

Thanks Stefan

nickloman commented 7 years ago

This seems to stem from a MinKNOW update (>=1.4) and is rather frustrating. We will need to put a specific check in for ISO formatted dates. If you could supply a new read to test again that would be helpful.

sengelen commented 7 years ago

Here is a fast5 file from MinKNOW 1.4 with /UniqueGlobalKey/tracking_id/exp_start_time in ISO format

I0014972_20170224_FNFAF05898_MN19040_sequencing_run_626_97325_ch99_read593_strand.fast5.gz

nickloman commented 7 years ago

Many thanks, fixed in latest commit https://github.com/arq5x/poretools/commit/af98d0b0fbb6172f659f2d5ea983b502cb35c65c