Export AIRR Fields for Dataset - AbXtract

Category Paths

  • Solution-based/Biologics/Antibody Design

  • Role-based/Bioinformatician

  • Role-based/Biologist

  • Product-based/AbXtract

  • Task-based/Data Science/Conversion

Description

Export AIRR fields from an existing dataset. Provides the option to convert AbXtract fields to AIRR-compatible fields for any AbXtract processed dataset, or return each row of the AIRR-compatible file associated with the records in a given dataset if the original file was AIRR-compatible.

Parameter title in user interface (promoted name)

  • Provide AbXtract cluster call in clone_id column (add_cluster_call) type: boolean: If AbXtract clustering was done and was_airr_input is TRUE (whereby original rows are returned),

inserts cluster call into the clone_id column. If was_airr_input is FALSE and clustering was performed, cluster call is automatically inserted in clone_id column, ignoring this parameter. If clustering was not performed, this parameter is ignored. If dataset is a result of Sanger processing and both cluster and clone_id column exist, the cluster column will overwrite the clone_id column.

Default: False

Parameter title in user interface (promoted name)

  • Count field for AIRR-compatible file (count_method) type: string: consensus_count field gives number of reads contributing to consensus sequence for a particular UMI. duplicate_count field gives number of UMIs sharing identical sequence or total number identical observationsof this sequence (absent UMIs). If dataset was generated from AIRR-comptabile file, choose the same field as was converted to ‘count’ in the AIRR-to-AbXtract file conversion.
    Default: duplicate_count
    Choices: consensus_count, duplicate_count

Parameter title in user interface (promoted name)

  • Dataset was produced from an AIRR-compatible file (was_airr_input) type: boolean: Dataset produced from file that had AIRR-compatible headers.
Set to FALSE if you would rather return AbXtract values with AIRR-compatible headers.
Default: False

Parameter title in user interface (promoted name)

  • Output CSV Filename (file_name) type: file_out: All records are written to downstream csv file, must contain the *.csv extension
    Default: airr_fields.csv

Parameter title in user interface (promoted name)

  • Failed Dataset Output Name (data_out) type: dataset_out: Contains failed records from both upstream and downstream processes
    Default: problematic.airr_fields