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arq5x / poretools

a toolkit for working with Oxford nanopore data
MIT License
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poretools 0.6.0 recursive access to all fast5 files in path #155

Closed splaisan closed 7 years ago

splaisan commented 7 years ago

duplicate of unanswered #151

My MinIon run returned a structure with subfolders in the 'fast5/pass' folder containing each 4000 fast5 files (created by MinKnow v 1.7.14). running on one folder of 4000 works but running commands fail so far to find the fast5 data from the 'pass' folder recursively. How can I run poretools apps on my 671'000 fast5 files in one go?

Thanks

===== poretools stats ../data/reads/DATA/fast5/pass/ WARNING:poretools:Directory is empty! WARNING:poretools:No valid sequences observed.

rem: adding */ at the end fails too

Thanks

arq5x commented 7 years ago

What version of poretools? This is implemented in the version in Github. Have you tried poretools stats ../data/reads/DATA/fast5/pass

splaisan commented 7 years ago

HI Aaron, After installing the github version over the pip installed 0.6.0 it worked out. Could it be that the PIP 0.6.0 differs from the github 0.6.0 (similarly to in #134; in which case could a subversion tag be added to the version when installing from the git cloned code)?

Thanks