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@@ -4,4 +4,5 @@ build | |
| .idea | ||
| data | ||
| docs/.vscode | ||
| __pycache__ | ||
| __pycache__ | ||
| .vscode | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,42 @@ | ||
| PSM_MAP = { | ||
| "sequence": "sequence", | ||
| #"opt_global_cv_MS:1000889_peptidoform_sequence": "peptidoform", | ||
| "modifications": "modifications", | ||
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| "opt_global_Posterior_Error_Probability_score": "posterior_error_probability", | ||
| "opt_global_q-value": "global_qvalue", | ||
| "opt_global_cv_MS:1002217_decoy_peptide": "is_decoy", | ||
| "calc_mass_to_charge": "calculated_mz", | ||
| "accession": "pg_accessions", | ||
| "unique": "unique", | ||
| "charge": "precursor_charge", | ||
| "exp_mass_to_charge": "observed_mz", | ||
| "retention_time": "rt", | ||
| } | ||
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| PSM_USECOLS = list(PSM_MAP.keys()) + [ | ||
| "spectra_ref", | ||
| "start", | ||
| "end", | ||
| "search_engine", | ||
| "search_engine_score[1]", | ||
| ] | ||
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| ADDITIONS = [ | ||
| "peptidoform", | ||
| "modification_details", | ||
| "additional_scores", | ||
| "pg_positions", | ||
| "protein_global_qvalue", | ||
| "gg_accessions", | ||
| "gg_names", | ||
| "predicted_rt" | ||
| "reference_file_name" | ||
| "scan_number" | ||
| "ion_mobility" | ||
| "num_peaks" | ||
| "mz_array" | ||
| "intensity_array" | ||
| "rank" | ||
| "cv_params" | ||
| ] |
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| import pyarrow as pa | ||
| PEPTIDE_FIELDS = [ | ||
| pa.field( | ||
| "sequence", | ||
| pa.string(), | ||
| metadata={"description": "The peptide’s sequence corresponding to the PSM"}, | ||
| ), | ||
| pa.field( | ||
| "peptidoform", | ||
| pa.string(), | ||
| metadata={"description": "Peptide sequence with modifications: Read the specification for more details"}, | ||
| ), | ||
| pa.field( | ||
| "modifications", | ||
| pa.list_(pa.string()), | ||
| metadata={"description": "List of modifications as string array, easy for search and filter"}, | ||
| ), | ||
| pa.field( | ||
| "modification_details", | ||
| pa.list_(pa.string()), | ||
| metadata={"description": "List of alternative site probabilities for the modification format: read the specification for more details"}, | ||
| ), | ||
| pa.field( | ||
| "posterior_error_probability", | ||
| pa.float32(), | ||
| metadata={"description": "Posterior error probability for the given peptide spectrum match"}, | ||
| ), | ||
| pa.field("global_qvalue", pa.float32(), metadata={"description": "Global q-value of the peptide or psm at the level of the experiment"}), | ||
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| pa.field( | ||
| "is_decoy", | ||
| pa.int32(), | ||
| metadata={"description": "Decoy indicator, 1 if the PSM is a decoy, 0 target"}, | ||
| ), | ||
| pa.field( | ||
| "calculated_mz", | ||
| pa.float32(), | ||
| metadata={"description": "Theoretical peptide mass-to-charge ratio based on identified sequence and modifications"}, | ||
| ), | ||
| pa.field( | ||
| "additional_scores", | ||
| pa.list_( | ||
| pa.struct([ | ||
| ("name", pa.string()), | ||
| ("score", pa.float32()) | ||
| ]) | ||
| ), | ||
| metadata={"description": "List of structures, each structure contains two fields: name and value"}, | ||
| ), | ||
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| pa.field( | ||
| "pg_accessions", | ||
| pa.list_(pa.string()), | ||
| metadata={"description": "Protein group accessions of all the proteins that the peptide maps to"}, | ||
| ), | ||
| pa.field( | ||
| "pg_positions", | ||
| pa.list_(pa.string()), | ||
| metadata={"description": "Protein start and end positions written as start_post:end_post"}, | ||
| ), | ||
| pa.field( | ||
| "unique", | ||
| pa.int32(), | ||
| metadata={"description": "Unique peptide indicator, if the peptide maps to a single protein, the value is 1, otherwise 0"}, | ||
| ), | ||
| pa.field( | ||
| "protein_global_qvalue", | ||
| pa.float32(), | ||
| metadata={"description": "Global q-value of the protein group at the experiment level"}, | ||
| ), | ||
| pa.field( | ||
| "gg_accessions", | ||
| pa.list_(pa.string()), | ||
| metadata={"description": "Gene accessions, as string array"}, | ||
| ), | ||
| pa.field( | ||
| "gg_names", | ||
| pa.list_(pa.string()), | ||
| metadata={"description": "Gene names, as string array"}, | ||
| ), | ||
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| pa.field( | ||
| "precursor_charge", | ||
| pa.int32(), | ||
| metadata={"description": "Precursor charge"}, | ||
| ), | ||
| pa.field( | ||
| "observed_mz", | ||
| pa.float32(), | ||
| metadata={"description": "Experimental peptide mass-to-charge ratio of identified peptide (in Da)"}, | ||
| ), | ||
| pa.field( | ||
| "rt", | ||
| pa.float32(), | ||
| metadata={"description": "MS2 scan’s precursor retention time (in seconds)"}, | ||
| ), | ||
| pa.field( | ||
| "predicted_rt", | ||
| pa.float32(), | ||
| metadata={"description": "Predicted retention time of the peptide (in seconds)"}, | ||
| ), | ||
| pa.field( | ||
| "quantmsio_version", | ||
| pa.string(), | ||
| metadata={"description": "The version of quantms.io"}, | ||
| ) | ||
| ] | ||
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| PSM_UNIQUE_FIELDS = [ | ||
| pa.field( | ||
| "reference_file_name", | ||
| pa.string(), | ||
| metadata={"description": "Spectrum file name with no path information and not including the file extension"}, | ||
| ), | ||
| pa.field( | ||
| "scan_number", | ||
| pa.string(), | ||
| metadata={"description": "Scan number of the spectrum"}, | ||
| ), | ||
| pa.field( | ||
| "ion_mobility", | ||
| pa.float32(), | ||
| metadata={"description": "Ion mobility value for the precursor ion"}, | ||
| ), | ||
| pa.field("num_peaks", pa.int32(), metadata={"description": "Number of peaks in the spectrum used for the peptide spectrum match"}), | ||
| pa.field( | ||
| "mz_array", | ||
| pa.list_(pa.float32()), | ||
| metadata={"description": "Array of m/z values for the spectrum used for the peptide spectrum match"}, | ||
| ), | ||
| pa.field( | ||
| "intensity_array", | ||
| pa.list_(pa.float32()), | ||
| metadata={"description": "Array of intensity values for the spectrum used for the peptide spectrum match"}, | ||
| ), | ||
| pa.field("rank", pa.int32(), metadata={"description": "Rank of the peptide spectrum match in the search engine output"}), | ||
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| pa.field( | ||
| "cv_params", | ||
| pa.list_( | ||
| pa.struct([ | ||
| ("name", pa.string()), | ||
| ("value", pa.string()) | ||
| ]) | ||
| ), | ||
| metadata={"description": "Optional list of CV parameters for additional metadata"}, | ||
| ), | ||
| ] | ||
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| PSM_FIELDS = PEPTIDE_FIELDS + PSM_UNIQUE_FIELDS |
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