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🐞 fix: TSNE now encodes query sequence correctly +++ fixed types in C… #22

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🐞 fix: TSNE now encodes query sequence correctly +++ fixed types in C… #22

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10 changes: 5 additions & 5 deletions scripts/ClusterMSA.py
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Original file line number Diff line number Diff line change
Expand Up @@ -50,10 +50,10 @@ def plot_landscape(x, y, df, query_, plot_type):
p.add_argument('--eps_val', action='store', type=float, help="Use single value for eps instead of scanning.")
p.add_argument('--resample', action='store_true', help='If included, will resample the original MSA with replacement before writing.')
p.add_argument("--gap_cutoff", action='store', type=float, default=0.25, help='Remove sequences with gaps representing more than this frac of seq.')
p.add_argument('--min_eps', action='store',default=3, help='Min epsilon value to scan for DBSCAN (Default 3).')
p.add_argument('--max_eps', action='store',default=20, help='Max epsilon value to scan for DBSCAN (Default 20).')
p.add_argument('--eps_step', action='store',default=.5, help='step for epsilon scan for DBSCAN (Default 0.5).')
p.add_argument('--min_samples', action='store',default=3, help='Default min_samples for DBSCAN (Default 3, recommended no lower than that).')
p.add_argument('--min_eps', action='store',default=3, type=int, help='Min epsilon value to scan for DBSCAN (Default 3).')
p.add_argument('--max_eps', action='store',default=20, type=int, help='Max epsilon value to scan for DBSCAN (Default 20).')
p.add_argument('--eps_step', action='store',default=.5, type=float, help='step for epsilon scan for DBSCAN (Default 0.5).')
p.add_argument('--min_samples', action='store',default=3, type=int, help='Default min_samples for DBSCAN (Default 3, recommended no lower than that).')

p.add_argument('--run_PCA', action='store_true', help='Run PCA on one-hot embedding of sequences and store in output_cluster_metadata.tsv')
p.add_argument('--run_TSNE', action='store_true', help='Run TSNE on one-hot embedding of sequences and store in output_cluster_metadata.tsv')
Expand Down Expand Up @@ -197,7 +197,7 @@ def plot_landscape(x, y, df, query_, plot_type):

if args.run_TSNE:
lprint('Running TSNE ...',f)
ohe_vecs = encode_seqs(df.sequence.tolist()+[query_.sequence.tolist()], max_len=L)
ohe_vecs = encode_seqs(df.sequence.tolist()+query_.sequence.tolist(), max_len=L)
# different than PCA because tSNE doesn't have .transform attribute

mdl = TSNE()
Expand Down