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ZhangLabTJU / fastBCR

A heuristic method for fast BCR clonal family inference from large-scale AIRR-seq data
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cannot open file 'ClonalTree/Examples/input/ClonalFamily_200.fasta' #4

Open royfrancis opened 2 months ago

royfrancis commented 2 months ago 
clonal.tree.generation(
  bcr_clusters = clus$merged_fasta, 
  index = 200, 
  raw_data = raw$merged_fasta, 
  python_path = "/opt/miniconda/envs/repair/bin/python"
)
use default substitution matrix
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file 'ClonalTree/Examples/input/ClonalFamily_200.fasta': No such file or directory

Update:

I manually create this folder:

mkdir -p ClonalTree/Examples/output

And that created a new file ClonalTree/Examples/input/ClonalFamily_200.fasta and then complained about this:

use default substitution matrix
/opt/miniconda/envs/repair/bin/python: can't open file 'ClonalTree/src/clonalTree.py': [Errno 2] No such file or directory

Update:

I had to download the python scripts in fastBCR/ClonalTree/src and then it worked.

ZhangLabTJU commented 2 months ago

ClonalTree is low-complexity and accurate approach to construct B-cell lineage trees that incorporates genotype abundances into minimum spanning tree (MST) algorithm to infer maximum parsimony trees (https://github.com/julibinho/ClonalTree). It is compiled using Python and we choose to use it as our default phylogenetic tree construction method. As you have already known, users should download the ’fastBCR/ClonalTree‘ folder to use ClonalTree normally.