Greg Caporaso gregcaporaso

Notes by Greg Caporaso ([email protected])

Analysis goals

From email to picrust-developers on 4 Oct 2012:

Filter the HMP (not HMP-mock) data set to ~50-100k sequences at random to form a filtered dataset (for decreased run time).
Select ~12 of the most abundant IMG-defined OTUs from the HMP, and slice the reference sequence to the amplified region in that dataset. "IMG-defined" here means that we have an IMG genome attached to the OTU, opposed to the Greengenes-defined OTUs where we don't have a genome for that specific OTU. "most abundant" will be somewhat arbitrary - I'm thinking something like a random 12 IMG-defined from the 25% most abundant OTUs in the dataset.

some other information.

Code for merging OTU tables in parallel. This code was written by Daniel McDonald.

	import os.path
	import smtplib
	from email.MIMEMultipart import MIMEMultipart
	from email.MIMEBase import MIMEBase
	from email.MIMEText import MIMEText
	from email import Encoders

	def mail(to, subject, text, mail_user, mail_password, attach=None):
	msg = MIMEMultipart()

	#!/usr/bin/env python
	from __future__ import division

	__author__ = "Logan Knecht"
	__copyright__ = "Copyright 2012, The QIIME project"
	__credits__ = ["Logan Knecht", "Michael Dwan", "Damien Coy", "Jai Ram Rideout",
	"Levi McCracken"]
	__license__ = "GPL"
	__version__ = "1.5.0-dev-svn3058-bugfix"
	__maintainer__ = "Jai Ram Rideout"

	#!/usr/bin/env python
	# File created on 19 Jul 2012
	from __future__ import division

	__author__ = "Greg Caporaso"
	__copyright__ = "Copyright 2011, The QIIME project"
	__credits__ = ["Greg Caporaso"]
	__license__ = "GPL"
	__version__ = "1.5.0-dev"
	__maintainer__ = "Greg Caporaso"

	#!/usr/bin/env python
	# File created on 03 Jul 2012
	from __future__ import division

	__author__ = "Greg Caporaso"
	__copyright__ = "Copyright 2011, The QIIME project"
	__credits__ = ["Greg Caporaso"]
	__license__ = "GPL"
	__version__ = "1.5.0-dev"
	__maintainer__ = "Greg Caporaso"