trouble with basset_motifs.py about basset HOT 4 CLOSED

It looks like there's a bug in the trim code. I uploaded a new version of the script that should fix it.

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Looks better thanks!

The TOMTOM html report is now generated nicely.

However, still worrying messages from the log ... :

Processing query 235 out of 235
Estimating pi_0 from all 1468 observed p-values.
Estimating pi_0.
Estimated pi_0=1
/home/ron/anaconda2/lib/python2.7/site-packages/sklearn/preprocessing/data.py:167: UserWarning: Numerical issues were encountered when centering the data and might not be solved. Dataset may contain too large values. You may need to prescale your features.
warnings.warn("Numerical issues were encountered "
/home/ron/anaconda2/lib/python2.7/site-packages/sklearn/preprocessing/data.py:184: UserWarning: Numerical issues were encountered when scaling the data and might not be solved. The standard deviation of the data is probably very close to 0.
warnings.warn("Numerical issues were encountered "
basset_motifs_predict.lua dnase_with_prim_erythroid_cnn_best.decuda.th motifs_out/sample.h5 motifs_out/model_out.h5
Filter 0
Filter 1

##########################################

Filter 296
Filter 297
Filter 298
Filter 299
6 segments of length 97
6 segments of length 97
Traceback (most recent call last):
File "/home/ron/tools/Basset/src/basset_motifs.py", line 668, in
main()
File "/home/ron/tools/Basset/src/basset_motifs.py", line 192, in main
plot_filter_seg_heat(filter_outs, '%s/filter_segs_raw.pdf'%options.out_dir, whiten=False)
File "/home/ron/tools/Basset/src/basset_motifs.py", line 516, in plot_filter_seg_heat
sns.clustermap(filter_seqs[:,seqs_i], metric=dist, row_cluster=True, col_cluster=True, linewidths=0, xticklabels=False, vmin=hmin, vmax=hmax)
File "/home/ron/anaconda2/lib/python2.7/site-packages/seaborn/matrix.py", line 1169, in clustermap
**kwargs)
File "/home/ron/anaconda2/lib/python2.7/site-packages/seaborn/matrix.py", line 1008, in plot
row_linkage=row_linkage, col_linkage=col_linkage)
File "/home/ron/anaconda2/lib/python2.7/site-packages/seaborn/matrix.py", line 941, in plot_dendrograms
axis=1, ax=self.ax_col_dendrogram, linkage=col_linkage)
File "/home/ron/anaconda2/lib/python2.7/site-packages/seaborn/matrix.py", line 684, in dendrogram
label=label, rotate=rotate)
File "/home/ron/anaconda2/lib/python2.7/site-packages/seaborn/matrix.py", line 502, in init
self.dendrogram = self.calculate_dendrogram()
File "/home/ron/anaconda2/lib/python2.7/site-packages/seaborn/matrix.py", line 582, in calculate_dendrogram
color_threshold=-np.inf)
File "/home/ron/anaconda2/lib/python2.7/site-packages/scipy/cluster/hierarchy.py", line 2230, in dendrogram
is_valid_linkage(Z, throw=True, name='Z')
File "/home/ron/anaconda2/lib/python2.7/site-packages/scipy/cluster/hierarchy.py", line 1412, in is_valid_linkage
name_str)
ValueError: Linkage 'Z' contains negative indices.

################

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I know I've seen that before, but I can't replicate it at the moment. I would guess that one of the filters isn't activating at all and causing the statistical code to choke. I never got much value out of those heat map plots, so I'm going to turn them off by default and keep my eye out for an opportunity to fix the bug next time that I see it.

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Sorry for the delay and thanks for the workaround, the same example now runs without complaints.

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