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Enable unique modus #38

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merged 2 commits into from
Nov 19, 2024
Merged

Enable unique modus #38

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7ced8b8
add minimum number of iterations
LaraFuhrmann Nov 10, 2024
822f341
pass unique_modus argument
LaraFuhrmann Nov 10, 2024
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2 changes: 1 addition & 1 deletion viloca/local_haplotype_inference/use_quality_scores/analyze_results.py
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ def haplotypes_to_fasta(state_curr_dict, output_dir):
ave_reads = state_curr_dict["weight" + str(k)]
if ave_reads==0:
# this haplotype will not be reported as there are no reads
# supporting it.
# supporting it.
continue

head = (
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5 changes: 3 additions & 2 deletions viloca/local_haplotype_inference/use_quality_scores/cavi.py
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Expand Up @@ -114,8 +114,9 @@ def run_cavi(
iter = 0
converged = False
elbo = 0
min_number_iterations = 10
state_curr_dict = state_init_dict
while converged is False:
while (converged is False) or (iter < min_number_iterations):

if iter <= 1:
digamma_alpha_sum = digamma(state_curr_dict["alpha"].sum(axis=0))
Expand Down Expand Up @@ -155,7 +156,7 @@ def run_cavi(
break
elif (history_elbo[-2] > elbo) and np.abs(elbo - history_elbo[-2]) > 1e-08:
exit_message = "Error: ELBO is decreasing."
break
#break
elif np.abs(elbo - history_elbo[-2]) < convergence_threshold:
converged = True
exit_message = "ELBO converged."
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10 changes: 5 additions & 5 deletions viloca/local_haplotype_inference/use_quality_scores/run_dpm_mfa.py
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Expand Up @@ -33,7 +33,7 @@ def main(
K,
alpha0,
alphabet="ACGT-",
unique_modus=False,
unique_modus=True,
convergence_threshold=1e-03,
):

Expand All @@ -46,7 +46,7 @@ def main(
reference_binary, ref_id = preparation.load_reference_seq(fref_in, alphabet)

reads_list, qualities = preparation.load_fasta_and_qualities(
freads_in, fname_qualities, alphabet, False
freads_in, fname_qualities, alphabet, unique_modus
)
reads_seq_binary, reads_weights = preparation.reads_list_to_array(reads_list)
reads_log_error_proba = preparation.compute_reads_log_error_proba(
Expand Down Expand Up @@ -147,9 +147,9 @@ def main(
sys.argv[1],
sys.argv[2],
sys.argv[3],
int(sys.argv[4]),
sys.argv[4],
int(sys.argv[5]),
float(sys.argv[6]),
sys.argv[7],
int(sys.argv[6]),
float(sys.argv[7]),
)
# freads_in, fref_in, output_dir, n_starts, K, alpha0, alphabet = 'ACGT-'
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