add_props_to_fq_files.py

Adds properties to FASTQ files in DNAnexus. Make sure you are logged into DNAnexus with the appropriate account before using this script in order to ensure access to the relevant projects. Accepts a tab-delimited input file containing properties to add to barcoded FASTQ files, and there must be a header line containing the two fields ‘dx_project_id’ and ‘barcode’. The remaining columns will be treated as property names. It is assumed that the directory containing the FASTQ files in each project is named /stage0_bcl2fastq/fastqs. Note that there are some standard property fields in use. For example, in the CIRM stem-cell project, the following property names are in use:

  1. lab_patient_id (i.e. some identifier for a give patient/sample)
  2. lab_patient_group (i.e. A categorization for the patient)
  3. lab_patient_condition (i.e. a treatment condition, perhaps a medicine and dosage)

The properties that represent FASTQ metadata for some lab protocol/setup should start with ‘lab’ followed by an underscore.

usage: add_props_to_fq_files.py [-h] -i INFILE

Named Arguments

-i, --infile Tab-delimited input file.