remove pymuscle5

tahiri-lab · Nov 6, 2023 · f508db3 · f508db3
1 parent a47d5b6
commit f508db3
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/aphylogeo/main.py b/aphylogeo/main.py
@@ -1,5 +1,5 @@
 import pandas as pd
-from aphylogeo.alignement import AlignSequences, Alignment
+from aphylogeo.alignement import AlignSequences
 
 from aphylogeo.params import Params
 from aphylogeo import utils
@@ -24,9 +24,9 @@
     sequenceFile = utils.loadSequenceFile(Params().reference_gene_file)
     seq_alignment = AlignSequences(sequenceFile).align()
     # Phylo.write(tree1, "data/tree1.nwk", "newick")
-    seq_alignment.save_to_json("./debug/sequences_aligned.json")
+    # seq_alignment.save_to_json("./debug/sequences_aligned.json")
 
-    loaded_seq_alignment = Alignment.load_from_json("./debug/sequences_aligned.json")
+    # loaded_seq_alignment = Alignment.load_from_json("./debug/sequences_aligned.json")
 
     geneticTrees = utils.geneticPipeline(seq_alignment.msa)
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -16,7 +16,7 @@ pyyaml = "^6.0.1"
 pytest = "^7.4.2"
 numpy = "^1.26.0"
 cython = "^3.0.2"
-pymuscle5 = {git = "https://github.com/althonos/pymuscle5"}
+#pymuscle5 = {git = "https://github.com/althonos/pymuscle5"}
 robinson-foulds = "^1.2"
 ete3 = "^3.1.3"
 dendropy = "^4.6.1"