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mamba env for installations; use compare --avg-containment --ani #1

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May 17, 2022
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mamba env for installations; use compare --avg-containment --ani #1

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2 changes: 1 addition & 1 deletion compare_matrices.py
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Original file line number Diff line number Diff line change
Expand Up @@ -84,7 +84,7 @@
subprocess.call(sketch_command, shell=True)
# Then run sourmash compare with ANI
save_prefix = 'sourmash_compare_ANI'
compare_ANI_command = f"sourmash compare -k 21 --ani -o {save_prefix}.cmp "
compare_ANI_command = f"sourmash compare -k 21 --ani --avg-containment -o {save_prefix}.cmp "
for _, gpath in genome_list:
sig_path = os.path.join(sketch_dir, gpath.split('/')[-1]) + '.sig'
compare_ANI_command += sig_path + ' '
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14 changes: 14 additions & 0 deletions environment.yml
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@@ -0,0 +1,14 @@
name: phylo-ani
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- sourmash=4.4
- biopython
- mmh3
# temporary: install sourmash 'latest' branch to get `--avg-containment`
- rust
- pip
- pip:
- git+https://github.com/sourmash-bio/sourmash@latest