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phbradley / conga

Clonotype Neighbor Graph Analysis
MIT License
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Hotfix/save distfile #13

Closed markgene closed 3 years ago

markgene commented 3 years ago

Hi there,

I fix the variable name of output distfile in function make_tcrdist_kernel_pcs_file_from_clones_file() to solve the error below: 

Using C++ TCRdist calculator
util.run_command: cmd= /CONGA_DIR/tcrdist_cpp/bin/find_neighbors -f clones_AB.dist_50_kpcs_tcrs.tsv --only_tcrdists -d /CONGA_DIR/tcrdist_cpp/db/tcrdist_info_mouse.txt -o clones_AB.dist_50_kpcs
Traceback (most recent call last):
  File "/CONGA_DIR/scripts/merge_samples.py", line 123, in <module>
    output_distfile=args.output_distfile )
  File "/CONGA_DIR/conga/preprocess.py", line 1343, in make_tcrdist_kernel_pcs_file_from_clones_file
    np.savetxt( distfile, D.astype(float), fmt='%.1f')
NameError: name 'distfile' is not defined

PS: thank you for developing CONGA!

-Mark