Merge pull request #119 from MannLabs/AX-989-add_quant_readers

Ax 989 add quant readers

Author: mschwoer

alphaquant/classify/ml_info_table.py

@@ -1,5 +1,5 @@
-import alphabase.quantification.quant_reader.config_dict_loader as ab_config_loader
-import alphabase.quantification.quant_reader.table_reformatter as ab_table_reformatter
+import alphaquant.quant_reader.config_dict_loader as ab_config_loader
+import alphaquant.quant_reader.table_reformatter as ab_table_reformatter
 import alphaquant.utils.reader_utils as aq_reader_utils
 
 import pandas as pd

alphaquant/config/config.py

@@ -1,5 +1,5 @@
 import logging
-import alphabase.quantification.quant_reader.config_dict_loader as ab_config_loader
+import alphaquant.quant_reader.config_dict_loader as ab_config_loader
 import os
 import re
 
@@ -14,6 +14,7 @@ def setup_logging():
 
 ############################################
 # Adapt some functions in the alphabase quant reader package
+# TODO: this was relevant only before the quant_readers were moved from alphabase, check if the methods can be overwritten
 
 def _get_seperator(input_file):
     filename = str(input_file)

alphaquant/diffquant/diffutils.py

@@ -392,9 +392,9 @@ def check_for_processed_runs_in_results_folder(results_folder):
 import os
 import pathlib
 
-import alphabase.quantification.quant_reader.config_dict_loader as abconfigdictloader
-import alphabase.quantification.quant_reader.longformat_reader as ablongformatreader
-import alphabase.quantification.quant_reader.wideformat_reader as abwideformatreader
+import alphaquant.quant_reader.config_dict_loader as abconfigdictloader
+import alphaquant.quant_reader.longformat_reader as ablongformatreader
+import alphaquant.quant_reader.wideformat_reader as abwideformatreader
 
 
 

alphaquant/ptm/ptmsite_mapping.py

@@ -1,7 +1,7 @@
 
 
 from alphaquant.config.variables import *
-import alphabase.quantification.quant_reader.config_dict_loader as abconfigdictloader
+import alphaquant.quant_reader.config_dict_loader as abconfigdictloader
 import alphaquant.resources.database_loader as aq_resource_dbloader
 
 import alphaquant.config.config as aqconfig

alphaquant/quant_reader/__init__.py

@@ -0,0 +1,127 @@
+import itertools
+import logging
+import os.path
+import pathlib
+import re
+
+import yaml
+
+from alphaquant.quant_reader import quantreader_utils
+
+LOGGER = logging.getLogger(__name__)
+INTABLE_CONFIG = os.path.join(pathlib.Path(__file__).parent.absolute(), "../config/quant_reader_config.yaml")
+
+
+
+def get_input_type_and_config_dict(input_file, input_type_to_use=None):
+    all_config_dicts = _load_config(INTABLE_CONFIG)
+    type2relevant_columns = _get_type2relevant_cols(all_config_dicts)
+
+    if "aq_reformat.tsv" in input_file:
+        input_file = _get_original_file_from_aq_reformat(input_file)
+
+    sep = _get_seperator(input_file)
+
+    uploaded_data_columns = quantreader_utils.read_columns_from_file(
+        input_file, sep=sep
+    )
+
+    for input_type in type2relevant_columns:
+        if (input_type_to_use is not None) and (input_type != input_type_to_use):
+            continue
+        relevant_columns = type2relevant_columns.get(input_type)
+        relevant_columns = [x for x in relevant_columns if x]  # filter None values
+        if set(relevant_columns).issubset(uploaded_data_columns):
+            config_dict = all_config_dicts.get(input_type)
+            return input_type, config_dict, sep
+
+    raise TypeError("format not specified in intable_config.yaml!")
+
+
+def _get_original_file_from_aq_reformat(input_file):
+    matched = re.match("(.*)(\..*\.)(aq_reformat\.tsv)", input_file)
+    return matched.group(1)
+
+
+def _get_seperator(input_file):
+    filename = str(input_file)
+    if ".csv" in filename:
+        return ","
+    elif ".tsv" in filename:
+        return "\t"
+    else:
+        LOGGER.info(
+            f"neither of the file extensions (.tsv, .csv) detected for file {input_file}! Trying with tab separation. In the case that it fails, please provide the correct file extension"
+        )
+    return "\t"
+
+
+def _load_config(config_yaml):
+    with open(config_yaml) as stream:
+        config_all = yaml.safe_load(stream)
+    return config_all
+
+
+def _get_type2relevant_cols(config_all):
+    type2relcols = {}
+    for type in config_all:
+        config_typedict = config_all.get(type)
+        relevant_cols = get_relevant_columns_config_dict(config_typedict)
+        type2relcols[type] = relevant_cols
+    return type2relcols
+
+
+def get_relevant_columns_config_dict(config_typedict):
+    filtcols = []
+    dict_ioncols = []
+    for filtconf in config_typedict.get("filters", {}).values():
+        filtcols.append(filtconf.get("param"))
+
+    if "ion_hierarchy" in config_typedict:
+        for headr in config_typedict.get("ion_hierarchy").values():
+            ioncols = list(itertools.chain.from_iterable(headr.get("mapping").values()))
+            dict_ioncols.extend(ioncols)
+
+    quant_ids = _get_quant_ids_from_config_dict(config_typedict)
+    sample_ids = _get_sample_ids_from_config_dict(config_typedict)
+    channel_ids = _get_channel_ids_from_config_dict(config_typedict)
+    relevant_cols = (
+        config_typedict.get("protein_cols")
+        + config_typedict.get("ion_cols", [])
+        + sample_ids
+        + quant_ids
+        + filtcols
+        + dict_ioncols
+        + channel_ids
+    )
+    relevant_cols = list(set(relevant_cols))  # to remove possible redudancies
+    return relevant_cols
+
+
+def _get_quant_ids_from_config_dict(config_typedict):
+    quantID = config_typedict.get("quant_ID")
+    if isinstance(quantID, str):
+        return [config_typedict.get("quant_ID")]
+    if quantID is None:
+        return []
+    else:
+        return list(config_typedict.get("quant_ID").values())
+
+
+def _get_sample_ids_from_config_dict(config_typedict):
+    sampleID = config_typedict.get("sample_ID")
+    if isinstance(sampleID, str):
+        return [config_typedict.get("sample_ID")]
+    if sampleID is None:
+        return []
+    else:
+        return config_typedict.get("sample_ID")
+
+
+def _get_channel_ids_from_config_dict(config_typedict):
+    return config_typedict.get("channel_ID", [])
+
+
+def import_config_dict():
+    config_dict = _load_config(INTABLE_CONFIG)
+    return config_dict