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Update quant reader config and table handling #129

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Merged
ammarcsj merged 2 commits into from
May 25, 2026
Merged

Update quant reader config and table handling #129

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ff6ba0e
Update quant reader config with new input types
ammarcsj May 25, 2026
fa84b3d
Update alphadia reader
ammarcsj May 25, 2026
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43 changes: 42 additions & 1 deletion alphaquant/config/quant_reader_config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -863,6 +863,9 @@ spectronaut_fragion_ms1_gene:
value: "True"
use_iontree: True
ml_level: CHARGE
variance_predictor_cols:
- EG.Cscore
- FG.ShapeQualityScore


spectronaut_fragion_ms1_gene:
Expand Down Expand Up @@ -912,6 +915,9 @@ spectronaut_fragion_ms1_gene:
value: 5.0
use_iontree: True
ml_level: CHARGE
variance_predictor_cols:
- EG.Cscore
- FG.ShapeQualityScore

spectronaut_precursor_fragion_ms1:
format: longtable
Expand Down Expand Up @@ -971,6 +977,9 @@ spectronaut_precursor_fragion_ms1:
value: "True"
use_iontree: True
ml_level: CHARGE
variance_predictor_cols:
- EG.Cscore
- FG.ShapeQualityScore


spectronaut_precursor_fragion_ms1:
Expand Down Expand Up @@ -1027,6 +1036,9 @@ spectronaut_precursor_fragion_ms1:
value: 5.0
use_iontree: True
ml_level: CHARGE
variance_predictor_cols:
- EG.Cscore
- FG.ShapeQualityScore


spectronaut_precursor_fragion_ms1_protein:
Expand Down Expand Up @@ -1083,6 +1095,9 @@ spectronaut_precursor_fragion_ms1_protein:
value: 5.0
use_iontree: True
ml_level: CHARGE
variance_predictor_cols:
- EG.Cscore
- FG.ShapeQualityScore


spectronaut_fragion_ms1_protein:
Expand Down Expand Up @@ -1132,6 +1147,9 @@ spectronaut_fragion_ms1_protein:
value: 5.0
use_iontree: True
ml_level: CHARGE
variance_predictor_cols:
- EG.Cscore
- FG.ShapeQualityScore
annotation_columns:
- PG.Genes

Expand Down Expand Up @@ -1170,6 +1188,9 @@ spectronaut_fragion_protein:
value: 5.0
use_iontree: True
ml_level: CHARGE
variance_predictor_cols:
- EG.Cscore
- FG.ShapeQualityScore
annotation_columns:
- PG.Genes

Expand Down Expand Up @@ -1342,8 +1363,25 @@ diaumpire_precursor_ms1:
ion_cols:
- Peptide Key

fragpipe_precursor:
format: widetable
quant_pre_or_suffix: " Intensity"
protein_cols:
- Protein
ion_hierarchy:
sequence_int:
order: [SEQ, MOD, CHARGE]
mapping:
SEQ:
- Peptide Sequence
MOD:
- Modified Sequence
CHARGE:
- Charge
use_iontree: False
ml_level: SEQ

fragpipe_precursors:
fragpipe_modseq:
format: widetable
quant_pre_or_suffix: " Intensity"
protein_cols:
Expand All @@ -1358,3 +1396,6 @@ fragpipe_precursors:
- Modified Sequence
use_iontree: False
ml_level: SEQ



3 changes: 1 addition & 2 deletions alphaquant/quant_reader/table_reformatter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -72,12 +72,11 @@ def merge_protein_cols_and_config_dict(

def join_columns(df, columns, separator="_"):
if len(columns) == 1:
return df[columns[0]].fillna("nan").infer_objects(copy=False).astype(str)
return df[columns[0]].fillna("nan").astype(str)
else:
return (
df[columns]
.fillna("nan")
.infer_objects(copy=False)
.astype(str)
.agg(separator.join, axis=1)
)
Expand Down
12 changes: 9 additions & 3 deletions alphaquant/tables/alphadia_reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,17 +26,23 @@ def __init__(self, fragment_matrix_file: str):
fragment_matrix_file (str): Path to the fragment matrix file
"""

self.ml_info_file = aq_utils.get_progress_folder_filename(fragment_matrix_file, ".ml_info_table.tsv")
self.ml_info_file = aq_utils.get_progress_folder_filename(fragment_matrix_file, ".ml_info_table.tsv.zip")
self.old_ml_info_file = aq_utils.get_progress_folder_filename(fragment_matrix_file, ".ml_info_table.tsv")
self.input_file_reformat = aq_utils.get_progress_folder_filename(fragment_matrix_file, ".alphadia_fragion.aq_reformat.tsv", remove_extension=False)

precursor_file = os.path.join(os.path.dirname(fragment_matrix_file), "precursors.tsv")
self._precursor_df = aq_reader_utils.read_file(precursor_file, sep="\t")
self._precursor2quantID = self._precursor2quantid()

if not os.path.exists(self.ml_info_file):
if os.path.exists(self.old_ml_info_file) and not os.path.exists(self.ml_info_file):
self.ml_info_file = self.old_ml_info_file
LOGGER.info(f"ML info file already exists at {self.ml_info_file}")
elif not os.path.exists(self.ml_info_file):
LOGGER.info(f"Creating ML info file")
self.ml_info_df = self._define_ml_info_table()
self.ml_info_df.to_csv(self.ml_info_file, sep="\t", index=False)
archive_name = os.path.basename(self.ml_info_file).removesuffix(".zip")
compression = {"method": "zip", "archive_name": archive_name}
self.ml_info_df.to_csv(self.ml_info_file, sep="\t", index=False, compression=compression)
else:
LOGGER.info(f"ML info file already exists at {self.ml_info_file}")

Expand Down
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