recurrent access still unsolved in the github version

[splaisan]

I open this case last year (https://github.com/arq5x/poretools/issues/155) but after a fresh install today notice that the recursive access to the subfolders of fast5 is not working for me.

My only fix was to create a folder with symlinks to the 500000 fast5 files which took time and is not really efficient.

My installed version using pip and or git and python ./setup.py install is 0.6.0 while the conda version is 0.6.1a1

I uninstalled with pip and installed with conda which returns 0.6.0 with --version BUT does the recursive search with a command like (fast5 being a folder of folders with no .fast5 in the base level)

poretools yield_plot --quiet --theme-bw --plot-type reads ./fast5 --saveas yield_plot.png

Is it possible that the git version (here) be outdated?

Thanks for looking into this

Stephane

PS: unless some old version is over-seeding the fresh install!!

[splaisan]

SideNote: after updating conda I get some warnings. Do not know if this is relevant here, just passing it At least now it parses recursively and produces plots

my command:

poretools yield_plot --quiet --theme-bw --plot-type basepairs ./fast5 --saveas yield_plot_bps.png

/opt/biotools/miniconda2/lib/python2.7/site-packages/h5py/__init__.py:36: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 88 from C header, got 96 from PyObject
  from ._conv import register_converters as _register_converters
/opt/biotools/miniconda2/lib/python2.7/site-packages/h5py/__init__.py:45: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 88 from C header, got 96 from PyObject
  from . import h5a, h5d, h5ds, h5f, h5fd, h5g, h5r, h5s, h5t, h5p, h5z
/opt/biotools/miniconda2/lib/python2.7/site-packages/h5py/_hl/group.py:22: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 88 from C header, got 96 from PyObject
  from .. import h5g, h5i, h5o, h5r, h5t, h5l, h5p
/opt/biotools/miniconda2/lib/python2.7/site-packages/pandas/_libs/__init__.py:4: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from .tslib import iNaT, NaT, Timestamp, Timedelta, OutOfBoundsDatetime
/opt/biotools/miniconda2/lib/python2.7/site-packages/pandas/__init__.py:26: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import (hashtable as _hashtable,
/opt/biotools/miniconda2/lib/python2.7/site-packages/pandas/core/dtypes/common.py:6: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import algos, lib
/opt/biotools/miniconda2/lib/python2.7/site-packages/pandas/core/util/hashing.py:7: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import hashing, tslib
/opt/biotools/miniconda2/lib/python2.7/site-packages/pandas/core/indexes/base.py:7: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import (lib, index as libindex, tslib as libts,
/opt/biotools/miniconda2/lib/python2.7/site-packages/pandas/tseries/offsets.py:21: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  import pandas._libs.tslibs.offsets as liboffsets
/opt/biotools/miniconda2/lib/python2.7/site-packages/pandas/core/ops.py:16: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import algos as libalgos, ops as libops
/opt/biotools/miniconda2/lib/python2.7/site-packages/pandas/core/indexes/interval.py:32: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs.interval import (
/opt/biotools/miniconda2/lib/python2.7/site-packages/pandas/core/internals.py:14: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import internals as libinternals
/opt/biotools/miniconda2/lib/python2.7/site-packages/pandas/core/sparse/array.py:33: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  import pandas._libs.sparse as splib
/opt/biotools/miniconda2/lib/python2.7/site-packages/pandas/core/window.py:36: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  import pandas._libs.window as _window
/opt/biotools/miniconda2/lib/python2.7/site-packages/pandas/core/groupby/groupby.py:68: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import (lib, reduction,
/opt/biotools/miniconda2/lib/python2.7/site-packages/pandas/core/reshape/reshape.py:30: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import algos as _algos, reshape as _reshape
/opt/biotools/miniconda2/lib/python2.7/site-packages/pandas/io/parsers.py:45: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  import pandas._libs.parsers as parsers
/opt/biotools/miniconda2/lib/python2.7/site-packages/pandas/io/pytables.py:50: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import algos, lib, writers as libwriters
/opt/biotools/miniconda2/lib/python2.7/site-packages/statsmodels/nonparametric/kde.py:22: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from .linbin import fast_linbin
/opt/biotools/miniconda2/lib/python2.7/site-packages/statsmodels/nonparametric/smoothers_lowess.py:11: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._smoothers_lowess import lowess as _lowess