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sc932 / ALE

Assembly Likelihood Estimator
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plotter problem #4

Closed shaqhsn closed 10 years ago

shaqhsn commented 11 years ago

Hi , I am trying to work with plotter ,it starts reading contigs and calculating parameters but after reading last contig it complains as follow

NODE_434_length_480_cov_22.547916 had (0.992157) thresholded. Traceback (most recent call last): File "/ALE/src/plotter3.py", line 979, in main() File "/ALE/src/plotter3.py", line 969, in main plot_histogram(meta_number, save_figure=save_figure, pdf_stream=pdf_stream) File "/ALE/src/plotter3.py", line 755, in plot_histogram max_val = numpy.max(input_data) File "/numpy/py27/1.6.1-gcc47/lib/python2.7/site-packages/numpy/core/fromnumeric.py", line 1832, in amax return _wrapit(a, 'max', axis, out) File "/numpy/py27/1.6.1-gcc47/lib/python2.7/site-packages/numpy/core/fromnumeric.py", line 37, in _wrapit result = getattr(asarray(obj),method)(_args, *_kwds) ValueError: zero-size array to maximum.reduce without identity

sc932 commented 10 years ago

The authors recommend using IGV to view the output.

http://www.broadinstitute.org/igv/

Just import the assembly, bam and ALE scores. You can convert the .ale file to a set of .wig files with ale2wiggle.py and IGV can read those directly. Depending on your genome size you may want to convert the .wig files to the BigWig format.

The internal, debugging plotter is not in active development and is no longer supported.