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ADD: export before scoring with MS1MS2 scores #87

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Dec 15, 2022
Merged

ADD: export before scoring with MS1MS2 scores #87

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12 changes: 12 additions & 0 deletions pyprophet/data_handling.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@
def profile(fun):
return fun

# selection of scores with low cross-correlation for metabolomics scoring
def use_metabolomics_scores():
return [
"var_ms1_isotope_overlap_score",
Expand All @@ -29,6 +30,17 @@ def use_metabolomics_scores():
"var_norm_rt_score"
]

# extracts the scores and writes it into an SQL command
# in some cases some post processing has to be performed depending on which
# position the statement should be inserted (e.g. export_compounds.py)
def write_scores_sql_command(con, score_sql, feature_name, var_replacement):
feature = pd.read_sql_query("""PRAGMA table_info(%s)""" % feature_name, con)
score_names_sql = [name for name in feature["name"].tolist() if name.startswith("VAR")]
score_names_lower = [name.lower().replace("var_", var_replacement) for name in score_names_sql]
for i in range(0,len(score_names_sql)):
score_sql = score_sql + str(feature_name + "." + score_names_sql[i] + " AS " + score_names_lower[i] + ", ")
return score_sql

# Parameter transformation functions
def transform_pi0_lambda(ctx, param, value):
if value[1] == 0 and value[2] == 0:
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