inspirewind
commented
1 week ago Based on the get_value function and the content of the CSV file, it appears that val is returning a Series because the same samplename and contig correspond to multiple seed and cov_sim values in the CSV.
To ensure a scalar value is returned, we can add logic to handle this situation in the get_value function. For example, if val is a Series, choose to return the first value or handle it in another way. Modify get_value as follows：
def get_value(table, wildcards, value):
if table not in table_cache:
df = pd.read_csv(
table,
sep="\t",
index_col=["samplename", "fasta", "contig"],
)
table_cache[table] = df
df = table_cache[table]
val = df.loc[wildcards.sample].loc[wildcards.fasta].loc[wildcards.contig][value]
print(f"[debug]: table: {table}")
print(f"[debug]: df: {df}")
print(f"[debug]: val: {val}")
if isinstance(val, pd.Series):
return val.iloc[0]
return val
farchaab
MeSS version mess 0.9.0 pyhdfd78af_0 bioconda Describe the bug [Sun Sep 29 14:55:46 2024] Finished job 7. 11 of 19 steps (58%) done InputFunctionException in rule art_illumina in file /home/inspirewind/miniconda3/envs/mess/lib/python3.12/site-packages/mess/workflow/rules/simulate/short_reads.smk, line 38: Error: TypeError: cannot convert the series to <class 'int'> Wildcards: sample=sample fasta=GCF_016127215.1 contig=NZ_CP065991.1 Traceback: File "/home/inspirewind/miniconda3/envs/mess/lib/python3.12/site-packages/mess/workflow/rules/simulate/short_reads.smk", line 49, in
File "/home/inspirewind/miniconda3/envs/mess/lib/python3.12/site-packages/pandas/core/series.py", line 248, in wrapper (rule art_illumina, line 38, /home/inspirewind/miniconda3/envs/mess/lib/python3.12/site-packages/mess/workflow/rules/simulate/short_reads.smk)
Minimal example
Additional context