batch_download_fastqs.py

Calls download_fastqs.py in batch, provided an input file specifying the FASTQs to download. This script passes a log file name to download_fastqs.py for error logging, i.e. if a DNAnexus project isn’t found then it will be logged. The log file is named after this script and contains the number of seconds since the epoch to help generate a unique name.

usage: batch_download_fastqs.py [-h] -i INFILE -d FILE_DOWNLOAD_DIR
                                [--not-found-error]

Named Arguments

-i, --infile

Tab-delimited input file in one of two formats. Empty lines and lines beginning with a ‘#’ will be skipped. The first line must be a header line. The first format is used if you don’t know the DNAnexus project. Format 1 has the following fields:

  1. uhts run name,
  2. sequencing lane,
  3. library name,
  4. barcode.

Format 2 has the following fields:

  1. dnanexus_project_name,
  2. barcode

The script will act on format 1 parsing rules if 4 Fields are detected in the header line, and those of the second format if two fields are detected in the header line. Any other number of fields found in the header line will result in an error.

A note on format 1, you don’t have to include values for each field. For unknown values, just leave it blank. These values are stored as properties on a DNAnexus project, and the search for a DNAnexus project will be successful if you supply enough property information to uniquely identify a project.

-d, --file-download-dir
 
Local directory in which to download the FASTQ files.
--not-found-error
 
Presence of this options means to raise an Exception if a project can’t be found on DNAnexus with the provided input.

Default: False