Support multi-level aggregation 1 | Streamline definition of PsmDfCols keys

.bumpversion.toml

@@ -1,5 +1,5 @@
 [tool.bumpversion]
-current_version = "1.7.3-dev0"
+current_version = "1.7.4-dev0"
 parse = """(?x)
     (?P<major>0|[1-9]\\d*)\\.
     (?P<minor>0|[1-9]\\d*)\\.

alphabase/__init__.py

@@ -1 +1 @@
-__version__ = "1.7.3-dev0"
+__version__ = "1.7.4-dev0"

alphabase/constants/const_files/psm_reader.yaml

@@ -200,6 +200,9 @@ diann: # 1.8.1
     'score': 'CScore'
     'fdr': 'Q.Value'
     'intensity': "PG.MaxLFQ"
+    "precursor_intensity": "Precursor.Normalised"
+    "precursor_id": "Precursor.Id"
+    "gene_intensity": "Genes.MaxLFQ"
     # extra columns for performing FDR cutoff
     'fdr1_search1': 'Global.Q.Value'  # first search
     'fdr2_search1': 'Global.PG.Q.Value'  # first search

alphabase/psm_reader/keys.py

@@ -20,7 +20,85 @@ def get_values(cls) -> List[str]:
 
 
 class PsmDfCols(metaclass=ConstantsClass):
-    """Constants for accessing the columns of a PSM dataframe."""
+    """Constants for accessing the columns of a PSM dataframe.
+
+    Attributes
+    ----------
+    MOD_SITES, MODIFIED_SEQUENCE
+        Peptide sequence annotated with modification locations and standardized modification labels.
+    SEQUENCE
+        Peptide amino-acid sequence without modification annotations (plain sequence of residues).
+    DECOY
+        Label indicating whether the matched sequence is a decoy (reverse/shuffled) entry used for FDR estimation.
+    MODS
+        List of modifications on the peptide in unimod standardization
+    SCORE
+        Primary identification score for the PSM produced by the search engine quantifying quality of the PSM in arbitrary units.
+    TO_REMOVE
+    AA_MASS_DIFFS
+    AA_MASS_DIFF_SITES
+    RT
+        Retention time of the precursor (time when the precursor eluted during chromatography) in [UNIT].
+    RT_START
+        Start of search window in retention time of the precursor (time when the precursor eluted during chromatography) in [UNIT].
+    RT_STOP
+        End of search window in retention time of the precursor (time when the precursor eluted during chromatography) in [UNIT].
+    RT_NORM
+        Normalized retention time of the precursor (time when the precursor eluted during chromatography) in [UNIT].
+    SPEC_IDX
+        Spectrum index or internal spectrum identifier used by some file formats/engines to reference a spectrum; may be distinct from scan number.
+    SCANNR
+        MS/MS scan number (integer) indexing the spectrum within the raw file; use to locate the spectrum in vendor files or mzML.
+    FDR
+        False discovery rate (FDR) or q-value associated with the PSM.
+    NAA
+        Number of amino acids in sequence
+    CCS
+        Collision Cross Section (CCS) value for the ion in [UNIT].
+    MOBILITY
+        Ion mobility value associated with the precursor when available in [UNIT].
+    PEPTIDE_FDR
+        FDR or q-value estimated at the peptide-sequence level.
+    PROTEIN_FDR
+        FDR or q-value estimated at the protein or protein-group level.
+    RAW_NAME
+        Original filename or run identifier as reported by the acquisition system or search engine.
+        Represents the raw data source that produced the spectrum.
+    CHARGE
+        Charge state of precursor.
+    PROTEINS
+        Protein names (human readable format) of the matching protein group.
+    INTENSITY
+        Intensity of the corresponding protein group.
+    SCAN_NUM
+        MS/MS scan number (integer) indexing the na within the raw file.
+    PRECURSOR_MZ
+        Measured precursor mass-to-charge ratio (m/z) for the MS/MS spectrum.
+    DIANN_SPEC_INDEX
+        Precursor.Lib.Index index of the precursor in the internal representation used by DIA-NN for the spectral library.
+    UNIPROT_IDS
+        Uniprot identifiers of the corresponding protein group.
+    GENES
+        Gene names (typically in HGNC nomenclature) of the corresponding protein group.
+    QUERY_ID
+    FDR1_SEARCH1
+        Empirical FDR cutoff for first-pass Global precursor Q-Value.
+    FDR2_SEARCH1
+        Empirical FDR cutoff for first-pass Global protein group Q-Value.
+    FDR1_SEARCH2
+        Empirical FDR cutoff for second pass spectral library precursor Q-Value.
+    FDR2_SEARCH2
+    PRECURSOR_ID
+        Unique identifier for each precursor, i.e. a physical ionized peptide species.
+    PRECURSOR_INTENSITY
+        Computed intensity value for a specific precursor, i.e. a physical ionized peptide species.
+    GENE_INTENSITY
+        Computed intensity value on a gene level.
+    PEPTIDE_INTENSITY
+        Computed intensity value on a peptide/sequence level.
+        Empirical FDR cutoff for second pass library protein group Q-Value.
+
+    """
 
     # TODO: these are used only in th psm_reader package and the spectral_library.reader module so far
     MOD_SITES = "mod_sites"
@@ -65,6 +143,13 @@ class PsmDfCols(metaclass=ConstantsClass):
     FDR1_SEARCH2 = "fdr1_search2"
     FDR2_SEARCH2 = "fdr2_search2"
 
+    PRECURSOR_ID = "precursor_id"
+    PRECURSOR_INTENSITY = "precursor_intensity"
+
+    GENE_INTENSITY = "gene_intensity"
+
+    PEPTIDE_INTENSITY = "peptide_intensity"
+
 
 class LibPsmDfCols(metaclass=ConstantsClass):
     """Constants for accessing the columns of a Library PSM dataframe."""

docs/conf.py

@@ -24,7 +24,7 @@
 copyright = "2022, Mann Labs, MPIB"
 author = "Mann Labs, MPIB"
 
-release = "1.7.3-dev0"
+release = "1.7.4-dev0"
 
 # -- General configuration ---------------------------------------------------