Parser for the .oswpq file

[jcharkow]

Create a new results file parser for the .oswpq file.

The .oswpq is a directory containing a precursors_features.parquet and a transition_features.parquet file

The specifications are as follows:

precursor_features.parquet Schema([ ('PROTEIN_ID', Int64), ('PEPTIDE_ID', Int64), ('IPF_PEPTIDE_ID', Int64), ('PRECURSOR_ID', Int64), ('PROTEIN_ACCESSION', String), ('UNMODIFIED_SEQUENCE', String), ('MODIFIED_SEQUENCE', String), ('PRECURSOR_TRAML_ID', String), ('PRECURSOR_GROUP_LABEL', String), ('PRECURSOR_MZ', Float64), ('PRECURSOR_CHARGE', Int64), ('PRECURSOR_LIBRARY_INTENSITY', Float64), ('PRECURSOR_LIBRARY_RT', Float64), ('PRECURSOR_LIBRARY_DRIFT_TIME', Float64), ('GENE_ID', Int64), ('GENE_NAME', String), ('GENE_DECOY', Int64), ('PROTEIN_DECOY', Int64), ('PEPTIDE_DECOY', Int64), ('PRECURSOR_DECOY', Int64), ('RUN_ID', Int64), ('FILENAME', String), ('FEATURE_ID', Int64), ('EXP_RT', Float64), ('EXP_IM', Float64), ('NORM_RT', Float64), ('DELTA_RT', Float64), ('LEFT_WIDTH', Float64), ('RIGHT_WIDTH', Float64), ('FEATURE_MS1_AREA_INTENSITY', Float64), ('FEATURE_MS1_APEX_INTENSITY', Float64), ('FEATURE_MS1_EXP_IM', Float64), ('FEATURE_MS1_DELTA_IM', Float64), ('FEATURE_MS1_VAR_MASSDEV_SCORE', Float64), ('FEATURE_MS1_VAR_MI_SCORE', Float64), ('FEATURE_MS1_VAR_MI_CONTRAST_SCORE', Float64), ('FEATURE_MS1_VAR_MI_COMBINED_SCORE', Float64), ('FEATURE_MS1_VAR_ISOTOPE_CORRELATION_SCORE', Float64), ('FEATURE_MS1_VAR_ISOTOPE_OVERLAP_SCORE', Float64), ('FEATURE_MS1_VAR_IM_MS1_DELTA_SCORE', Float64), ('FEATURE_MS1_VAR_XCORR_COELUTION', Float64), ('FEATURE_MS1_VAR_XCORR_COELUTION_CONTRAST', Float64), ('FEATURE_MS1_VAR_XCORR_COELUTION_COMBINED', Float64), ('FEATURE_MS1_VAR_XCORR_SHAPE', Float64), ('FEATURE_MS1_VAR_XCORR_SHAPE_CONTRAST', Float64), ('FEATURE_MS1_VAR_XCORR_SHAPE_COMBINED', Float64), ('FEATURE_MS2_AREA_INTENSITY', Float64), ('FEATURE_MS2_TOTAL_AREA_INTENSITY', Float64), ('FEATURE_MS2_APEX_INTENSITY', Float64), ('FEATURE_MS2_EXP_IM', Float64), ('FEATURE_MS2_EXP_IM_LEFTWIDTH', Float64), ('FEATURE_MS2_EXP_IM_RIGHTWIDTH', Float64), ('FEATURE_MS2_DELTA_IM', Float64), ('FEATURE_MS2_TOTAL_MI', Float64), ('FEATURE_MS2_VAR_BSERIES_SCORE', Float64), ('FEATURE_MS2_VAR_DOTPROD_SCORE', Float64), ('FEATURE_MS2_VAR_INTENSITY_SCORE', Float64), ('FEATURE_MS2_VAR_ISOTOPE_CORRELATION_SCORE', Float64), ('FEATURE_MS2_VAR_ISOTOPE_OVERLAP_SCORE', Float64), ('FEATURE_MS2_VAR_LIBRARY_CORR', Float64), ('FEATURE_MS2_VAR_LIBRARY_DOTPROD', Float64), ('FEATURE_MS2_VAR_LIBRARY_MANHATTAN', Float64), ('FEATURE_MS2_VAR_LIBRARY_RMSD', Float64), ('FEATURE_MS2_VAR_LIBRARY_ROOTMEANSQUARE', Float64), ('FEATURE_MS2_VAR_LIBRARY_SANGLE', Float64), ('FEATURE_MS2_VAR_LOG_SN_SCORE', Float64), ('FEATURE_MS2_VAR_MANHATTAN_SCORE', Float64), ('FEATURE_MS2_VAR_MASSDEV_SCORE', Float64), ('FEATURE_MS2_VAR_MASSDEV_SCORE_WEIGHTED', Float64), ('FEATURE_MS2_VAR_MI_SCORE', Float64), ('FEATURE_MS2_VAR_MI_WEIGHTED_SCORE', Float64), ('FEATURE_MS2_VAR_MI_RATIO_SCORE', Float64), ('FEATURE_MS2_VAR_NORM_RT_SCORE', Float64), ('FEATURE_MS2_VAR_XCORR_COELUTION', Float64), ('FEATURE_MS2_VAR_XCORR_COELUTION_WEIGHTED', Float64), ('FEATURE_MS2_VAR_XCORR_SHAPE', Float64), ('FEATURE_MS2_VAR_XCORR_SHAPE_WEIGHTED', Float64), ('FEATURE_MS2_VAR_YSERIES_SCORE', Float64), ('FEATURE_MS2_VAR_ELUTION_MODEL_FIT_SCORE', Float64), ('FEATURE_MS2_VAR_IM_XCORR_SHAPE', Float64), ('FEATURE_MS2_VAR_IM_XCORR_COELUTION', Float64), ('FEATURE_MS2_VAR_IM_DELTA_SCORE', Float64), ('FEATURE_MS2_VAR_SONAR_LAG', Float64), ('FEATURE_MS2_VAR_SONAR_SHAPE', Float64), ('FEATURE_MS2_VAR_SONAR_LOG_SN', Float64), ('FEATURE_MS2_VAR_SONAR_LOG_DIFF', Float64), ('FEATURE_MS2_VAR_SONAR_LOG_TREND', Float64), ('FEATURE_MS2_VAR_SONAR_RSQ', Float64), ('SCORE_MS2_SCORE', Float64), ('SCORE_MS2_PEAK_GROUP_RANK', Float64), ('SCORE_MS2_P_VALUE', Float64), ('SCORE_MS2_Q_VALUE', Float64), ('SCORE_MS2_PEP', Float64), ('SCORE_IPF_PRECURSOR_PEAKGROUP_PEP', Float64), ('SCORE_IPF_QVALUE', Float64), ('SCORE_IPF_PEP', Float64), ('SCORE_PEPTIDE_RUN_SPECIFIC_SCORE', Float64), ('SCORE_PEPTIDE_RUN_SPECIFIC_P_VALUE', Float64), ('SCORE_PEPTIDE_RUN_SPECIFIC_Q_VALUE', Float64), ('SCORE_PEPTIDE_RUN_SPECIFIC_PEP', Float64) ])

transition_features.parquet Schema([ ('RUN_ID', Int64), ('IPF_PEPTIDE_ID', Int64), ('PRECURSOR_ID', Int64), ('TRANSITION_ID', Int64), ('TRANSITION_TRAML_ID', String), ('PRODUCT_MZ', Float64), ('TRANSITION_CHARGE', Int64), ('TRANSITION_TYPE', String), ('TRANSITION_ORDINAL', Int64), ('ANNOTATION', String), ('TRANSITION_DETECTING', Int64), ('TRANSITION_LIBRARY_INTENSITY', Float64), ('TRANSITION_DECOY', Int64), ('FEATURE_ID', Int64), ('FEATURE_TRANSITION_AREA_INTENSITY', Float64), ('FEATURE_TRANSITION_TOTAL_AREA_INTENSITY', Float64), ('FEATURE_TRANSITION_APEX_RT', Float64), ('FEATURE_TRANSITION_APEX_INTENSITY', Float64), ('FEATURE_TRANSITION_RT_FWHM', Float64), ('FEATURE_TRANSITION_MASSERROR_PPM', Float64), ('FEATURE_TRANSITION_TOTAL_MI', Float64), ('FEATURE_TRANSITION_VAR_INTENSITY_SCORE', Float64), ('FEATURE_TRANSITION_VAR_INTENSITY_RATIO_SCORE', Float64), ('FEATURE_TRANSITION_VAR_LOG_INTENSITY', Float64), ('FEATURE_TRANSITION_VAR_XCORR_COELUTION', Float64), ('FEATURE_TRANSITION_VAR_XCORR_SHAPE', Float64), ('FEATURE_TRANSITION_VAR_LOG_SN_SCORE', Float64), ('FEATURE_TRANSITION_VAR_MASSDEV_SCORE', Float64), ('FEATURE_TRANSITION_VAR_MI_SCORE', Float64), ('FEATURE_TRANSITION_VAR_MI_RATIO_SCORE', Float64), ('FEATURE_TRANSITION_VAR_ISOTOPE_CORRELATION_SCORE', Float64), ('FEATURE_TRANSITION_VAR_ISOTOPE_OVERLAP_SCORE', Float64), ('FEATURE_TRANSITION_START_POSITION_AT_5', Float64), ('FEATURE_TRANSITION_END_POSITION_AT_5', Float64), ('FEATURE_TRANSITION_START_POSITION_AT_10', Float64), ('FEATURE_TRANSITION_END_POSITION_AT_10', Float64), ('FEATURE_TRANSITION_START_POSITION_AT_50', Float64), ('FEATURE_TRANSITION_END_POSITION_AT_50', Float64), ('FEATURE_TRANSITION_TOTAL_WIDTH', Float64), ('FEATURE_TRANSITION_TAILING_FACTOR', Float64), ('FEATURE_TRANSITION_ASYMMETRY_FACTOR', Float64), ('FEATURE_TRANSITION_SLOPE_OF_BASELINE', Float64), ('FEATURE_TRANSITION_BASELINE_DELTA_2_HEIGHT', Float64), ('FEATURE_TRANSITION_POINTS_ACROSS_BASELINE', Float64), ('FEATURE_TRANSITION_POINTS_ACROSS_HALF_HEIGHT', Float64), ('FEATURE_TRANSITION_EXP_IM', Float64), ('FEATURE_TRANSITION_EXP_IM_LEFTWIDTH', Float64), ('FEATURE_TRANSITION_EXP_IM_RIGHTWIDTH', Float64), ('FEATURE_TRANSITION_DELTA_IM', Float64), ('FEATURE_TRANSITION_VAR_IM_DELTA_SCORE', Float64), ('FEATURE_TRANSITION_VAR_IM_LOG_INTENSITY', Float64), ('FEATURE_TRANSITION_VAR_IM_XCORR_COELUTION_CONTRAST', Binary), ('FEATURE_TRANSITION_VAR_IM_XCORR_SHAPE_CONTRAST', Binary), ('FEATURE_TRANSITION_VAR_IM_XCORR_COELUTION_COMBINED', Binary), ('FEATURE_TRANSITION_VAR_IM_XCORR_SHAPE_COMBINED', Binary), ('SCORE_TRANSITION_SCORE', Float32), ('SCORE_TRANSITION_RANK', UInt32), ('SCORE_TRANSITION_P_VALUE', Float64), ('SCORE_TRANSITION_Q_VALUE', Float64), ('SCORE_TRANSITION_PEP', Float64) ])

You should create a OSWPQResultsAccess.py file and allow OSWPQResults to be accepted as the results file in any of the loaders