bbcflib::daflims Namespace Reference

Classes
class	DAFLIMS

---

Detailed Description

=======================
Module: bbcflib.daflims
=======================

The DNA Array Facility at the University of Lausanne provides all
their data in a LIMS accessible from VITAL-IT.  This module hides the
details of fetching files from that LIMS.  Files are identified by
four fields:

  * The facility where they were generated (either ``'lgtf'`` for Lausanne,
    or ``'gva'`` at the University of Geneva).

  * The machine at the facility on which they were generated (``'R2D2'`` or
    ``'C3PO'`` in Lausanne, or ``'HWUSI-EAS691'`` in Geneva).

  * The run number on that machine (an integer).

  * The lane in that run (also an integer).

Connecting to the LIMS requires a username and password, and will
often only be possible from certain hosts.  A connection is
represented as a DAFLIMS object, which provides methods for fetching
the three kinds of files stored in the LIMS:

  * ``fetch_fastq``: The FASTQ file of all reads.  You probably want
    this.

  * ``fetch_export``: The output of aligning all reads against some
    genome with Eland, a proprietary tool from Illumina.

  * ``fetch_qc``: pdf file of the QC.

For example, to fetch the FASTQ file of run 91, lane 3 sequenced on
R2D2 in Lausanne, write::

    d = DAFLIMS(username=..., password=...)
    d.fetch_fastq('lgtf', 'R2D2', 91, 3, '/path/to/save/to.fastq')

The last argument works much like a target given to the Unix command
``cp``: if it specifies a directory, the file is given a random name
in that directory.  If it is given a filename, the file is written to
that name.  If the last argument is omitted, the file is written to a
random name in the current working irectory.

  .. autoclass:: DAFLIMS