Subset the Number of Fields for Export - AbXtract

Category Paths

Follow one of these paths in the Orion user interface, to find the floe.

  • Solution-based/Biologics/Antibody Design

  • Role-based/Bioinformatician

  • Role-based/Biologist

  • Product-based/AbXtract

  • Task-based/Data Science/Conversion

Description

Select a subset of all fields for Export. If for any reason, the field is not present in the dataset the Floe will ignore it and include only those fields that are present.

Titles of required parameters (promoted names)

  • Output CSV Filename (file_name) type: file_out: All records are written to downstream csv file, must contain the CSV extension
    Default: subset_fields.csv
  • Identifier Fields to Keep (id_fields) type: string: NOTE: Sanger Well ID (if used) is specified by the ‘id’ field
    Default: [‘seq_id’, ‘barcode_group’]
    Choices: id, sample_name, barcode_group, barcode_round, processed_roi, overlay_roi, seq_id
  • Sequence Fields to Keep (string_fields) type: string:
    Default: [‘match_name_1’, ‘match_name_2’, ‘sequence_aa_1’, ‘sequence_aa_2’, ‘cdr3_aa_1’, ‘cdr3_aa_2’, ‘read’]
    Choices: read, sequence_1, sequence_aa_1, sequence_aa_1_2, match_name_1, match_name_1_2, fr1_1, fr2_1, fr3_1, fr4_1, cdr1_1, cdr2_1, cdr3_1, fr1_aa_1, fr2_aa_1, fr3_aa_1, fr4_aa_1, cdr1_aa_1, cdr2_aa_1, cdr3_aa_1, merged_cdrs_1, merged_cdrs_2, merged_cdrs_1_2, sequence_2, sequence_aa_2, match_name_2, fr1_2, fr2_2, fr3_2, fr4_2, cdr1_2, cdr2_2, cdr3_2, fr1_aa_2, fr2_aa_2, fr3_aa_2, fr4_aa_2, cdr1_aa_2, cdr2_aa_2, cdr3_aa_2
  • Output Name of the Subsetted Dataset (data_out) type: dataset_out: Name of the exported dataset
    Default: subset_fields
  • Failed Dataset Output Name (data_out) type: dataset_out: Contains failed records from both upstream and downstream processes
    Default: problematic.export_subselected_abxtract

Optional parameters (promoted names)

  • Experimental Fields to Keep, If Present (assay_stats) type: string:
    Default: []
    Choices: KD, on_rate, off_rate
  • Biophysical Fields to Keep (biophysical_stats) type: string:
    Default: []
    Choices: cdr3_aa_1_charge, cdr3_aa_1_hydropathy, cdr3_aa_1_length, merged_cdrs_1_hydropathy, merged_cdrs_2_hydropathy, merged_cdrs_1_2_hydropathy, merged_cdrs_1_charge, merged_cdrs_2_charge, merged_cdrs_1_2_charge, merged_cdrs_1_length, merged_cdrs_2_length, merged_cdrs_1_2_length, cdr3_aa_2_charge, cdr3_aa_2_hydropathy, cdr3_aa_2_length, N_philic, N_phobic, isoelectric_point, charge_symmetric_parameter, high_viscosity_index
  • Cluster Fields to Keep (cluster_fields) type: string:
    Default: [‘cluster’]
    Choices: cluster_cdr3_1, cluster_cdr3_2, cluster, cluster_numeric
  • Liability Fields to Keep (liability_stats) type: string:
    Default: []
    Choices: liability_string_cdr1_aa_1, liability_string_cdr2_aa_1, liability_string_cdr3_aa_1, liability_string_cdr1_aa_2, liability_string_cdr2_aa_2, liability_string_cdr3_aa_2, liability_quant_cdr1_aa_1, liability_quant_cdr2_aa_1, liability_quant_cdr3_aa_1, liability_quant_cdr1_aa_2, liability_quant_cdr2_aa_2, liability_quant_cdr3_aa_2, liability_quant_chain_1, liability_quant_chain_2, liability_quant_lcdr1_3_hcdr1_3
  • Population Fields to Keep (population_stats) type: string:
    Default: [‘percent_roi_final’]
    Choices: count, count_roi_final, count_roi_early, percent_roi_early, percent_roi_final, fold_enrichment_roi, log2_enrichment_roi, overlap_population, count_fl_final, count_fl_early, percent_fl_final, percent_fl_early, percent_fl, ratio_to_top_early, ratio_to_top_final, ratio_to_top_early_final
  • Sanger Overlap Fields to Keep (sanger_stats) type: string: These items indicate overlap of NGS to Sanger based on the specified region of interest (ROI)
    Default: []
    Choices: well_id, overlap_to_sanger, overlap_to_ngs
  • Quality Fields to Keep (sequence_functional_status) type: string:
    Default: []
    Choices: functional_1, sequence_issue, votes_1, functional_2, votes_2