Closed sschattgen closed 1 year ago
Hi Koshlan,
I'm trying to build trees using human gd TCRs and I'm encountering the following issue. I believe it is related to being gd data since I can use it with ab ok. Thoughts?
tr = TCRrep(cell_df = df, organism = 'human', chains = ['gamma'], db_file = 'alphabeta_gammadelta_db.tsv') tcrtree = TCRtree(tcrrep = tr, html_name = 'BM_gdTCR_ALL.html') tcrtree.build_tree()
['subject', 'mean_dist', 'pct_dist_75', 'pct_dist_50', 'pct_dist_25', 'fuzzy_simpson_diversity_75', 'fuzzy_simpson_diversity_50', 'fuzzy_simpson_diversity_25', 'cdr3_g_aa', 'v_g_gene', 'j_g_gene', 'svg_gamma', 'svg_raw_gamma', 'ref_size_gamma', 'ref_unique_gamma', 'percent_missing_gamma'] --------------------------------------------------------------------------- UnboundLocalError Traceback (most recent call last) Untitled-6 in <module> <a href='untitled:Untitled-6?line=37'>38</a> html_name = 'BM_gdTCR_ALL_gamma.html') <a href='untitled:Untitled-6?line=38'>39</a> ---> <a href='untitled:Untitled-6?line=39'>40</a> tcrtree.build_tree() c:\ProgramData\Anaconda3\envs\tcrdist3\lib\site-packages\tcrdist\tree.py in build_tree(self) 124 125 print(self.default_plot_hclust_props['tooltip_cols']) --> 126 _auto_hdiff2( tcrrep = self.tcrrep, 127 html_name = self.html_name, 128 pwmat_str_b = self.pwmat_str_b, c:\ProgramData\Anaconda3\envs\tcrdist3\lib\site-packages\tcrdist\tree.py in _auto_hdiff2(tcrrep, html_name, pwmat_str_b, pwmat_str_a, single, generate_svgs, combine_olga, verbose, prune, default_hcluster_diff_kwargs, default_member_summ_kwargs, default_plot_hclust_props) 354 355 if default_hcluster_diff_kwargs['pwmat'] is None: --> 356 if verbose : print(f"pwmat set with {pwmat_str}") 357 default_hcluster_diff_kwargs['pwmat'] = getattr(tcrrep, pwmat_str) 358 else: UnboundLocalError: local variable 'pwmat_str' referenced before assignment
Currently TCRtree only works with alpha/beta TCRs
Hi Koshlan,
I'm trying to build trees using human gd TCRs and I'm encountering the following issue. I believe it is related to being gd data since I can use it with ab ok. Thoughts?