Open zenghk opened 5 years ago
yana-safonova
commented
5 years ago Hi zenghk ,
Thank you for reporting the issue! Could you please attach your input CDR3 sequences to this thread so I can run IgScout and reproduce the bug?
Best regards, Yana
zenghk
commented
5 years ago SRR3099459.zip
The cdr3 file I used is uploaded. I find the previous problem can be solved by removing the step sns.heatmap in OutputDDMatirx function, and I calculate the result by myself. I also meet the problem in the following, But I can get part of the result and I cannot make sure I get the whole result.
The usage of my command is python igscout-master/tandem_cdr3_finder.py igscout-master/germline_data/human/IGHD.fa SRR3099459.fasta result_SRR3099459
and I meet the problem
File "igscout-master/tandem_cdr3_finder.py", line 595, in
The version of my python and some of the module is listed: python 2.7.8 seaborn 0.9.0 numpy 1.16.4 pandas 0.24.2 matplotlib 3.0.2 biopython 1.73
Traceback (most recent call last): File "igscout-master/tandem_cdr3_finder.py", line 561, in
OutputDDMatrix(d_genes, all_ds, tandem_ds, os.path.join(output_dir, "dd_heatmap.pdf"), label)
File "igscout-master/tandem_cdr3_finder.py", line 204, in OutputDDMatrix
sns.heatmap(matrix, cmap = 'jet', xticklabels = all_ds, yticklabels = all_ds, annot = np.array(annot_matrix), fmt = '', cbar = False, square = True, linewidth = .1, linecolor = 'grey', annot_kws = {'size' : 10})
File "/zzh_gpfs/apps/python/lib/python2.7/site-packages/seaborn/matrix.py", line 446, in heatmap
plotter.plot(ax, cbar_ax, kwargs)
File "/zzh_gpfs/apps/python/lib/python2.7/site-packages/seaborn/matrix.py", line 235, in plot
if self.annot:
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
I am using the dataset downloaded from SRA. But I meet the problem above, I use the Bioproject PRJNA308641 to test the script and meet the same problem, the CDR3 region is extracted according to the result MIXCR and default D reference is used.