bbcflib::daflims::DAFLIMS Class Reference

List of all members.

Public Member Functions
def	__init__
def	fetch_fastq
def	fetch_export
def	fetch_qc
Public Attributes
	username
	password
	url_opener

---

Detailed Description

Connect to the DNA Array Facility's LIMS.

Either specify *username* and *password*, or provide a
``ConfigParser`` object to the *config* argument.  The
ConfigParser should define ``daflims_username`` and
``daflims_password`` in the sections ``daflims`` (you can override
the section with the *section* argument).  If you specify a
*config* argument, and one or both of *username* and *password*,
the latter override the ConfigParser.

  .. py:method:: fetch_fastq(facility, machine, run, lane, to=None)

  .. py:method:: fetch_export(facility, machine, run, lane, to=None)

  .. automethod:: fetch_qc

---

Member Function Documentation

def bbcflib::daflims::DAFLIMS::fetch_export	(		self,
			facility,
			machine,
			run,
			lane,
			to = None
	)

Fetch a file from the LIMS to *to*.

If *to* is omitted, then the data is written to a
randomly named file in the current working directory.  If
*to* is a directory, the data is written to a randomly named
file in that directory.  Otherwise *to* is taken as the full
path to the file to write to.

The return value is a dictionary containing the following keys
(all of which refer to strings unless otherwise noted.

  * ``'path'`` (the path to the fetched file)
  * ``'machine'``
  * ``'run'`` (integer)
  * ``'lane'`` (integer)
  * ``'cycle'`` (integer)
  * ``'quantity (/pM)'`` (float, the concentration of DNA in picomolar)
  * ``'library'``
  * ``'project'``
  * ``'protocol'``
  * ``'run type'`` (``'ChipSeq'``, etc.)
  * ``'PI firstname'``
  * ``'PI lastname'``
  * ``'submitter firstname'``
  * ``'submitter lastname'``
  * ``'organism'``
  * ``'NCBI ID'`` (the genome Eland aligns against)

def bbcflib::daflims::DAFLIMS::fetch_fastq	(		self,
			facility,
			machine,
			run,
			lane,
			to = None,
			libname = None
	)

Fetch a file from the LIMS to *to*.

If *to* is omitted, then the data is written to a
randomly named file in the current working directory.  If
*to* is a directory, the data is written to a randomly named
file in that directory.  Otherwise *to* is taken as the full
path to the file to write to.

The return value is a dictionary containing the following keys
(all of which refer to strings unless otherwise noted.

  * ``'path'`` (the path to the fetched file)
  * ``'machine'``
  * ``'run'`` (integer)
  * ``'lane'`` (integer)
  * ``'cycle'`` (integer)
  * ``'quantity (/pM)'`` (float, the concentration of DNA in picomolar)
  * ``'library'``
  * ``'project'``
  * ``'protocol'``
  * ``'run type'`` (``'ChipSeq'``, etc.)
  * ``'PI firstname'``
  * ``'PI lastname'``
  * ``'submitter firstname'``
  * ``'submitter lastname'``
  * ``'organism'``
  * ``'NCBI ID'`` (the genome Eland aligns against)

def bbcflib::daflims::DAFLIMS::fetch_qc	(		self,
			facility,
			machine,
			run,
			lane,
			to = None
	)

Fetch a file from the LIMS to *to*.

If *to* is omitted, then the data is written to a
randomly named file in the current working directory.  If
*to* is a directory, the data is written to a randomly named
file in that directory.  Otherwise *to* is taken as the full
path to the file to write to.

The return value is a dictionary containing the following keys
(all of which refer to strings unless otherwise noted.

  * ``'path'`` (the path to the fetched file)
  * ``'machine'``
  * ``'run'`` (integer)
  * ``'lane'`` (integer)
  * ``'cycle'`` (integer)
  * ``'quantity (/pM)'`` (float, the concentration of DNA in picomolar)
  * ``'library'``
  * ``'project'``
  * ``'protocol'``
  * ``'run type'`` (``'ChipSeq'``, etc.)
  * ``'PI firstname'``
  * ``'PI lastname'``
  * ``'submitter firstname'``
  * ``'submitter lastname'``
  * ``'organism'``
  * ``'NCBI ID'`` (the genome Eland aligns against)

---

The documentation for this class was generated from the following file:

• /home/rougemon/Data/pipelines/libv2/bbcflib/bbcflib/daflims.py