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gregcaporaso / mgrast_fnas_to_qiime_fna.py
Created July 8, 2012 17:06
Script to convert a group of MG-RAST files into a single seqs.fna file for use with QIIME
#!/usr/bin/env python
# File created on 26 Jun 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"
@gregcaporaso
gregcaporaso / summarize_barcodes.py
Created July 10, 2012 17:07
Script for summarizing barcode error in the 'ultra-deep' ANL sequencing run
#!/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"
@gregcaporaso
gregcaporaso / qiime_to_humann.py
Created July 20, 2012 02:14
Quick-and-dirty script to take combined bl6 file and split it into per-metagenome bl6 files.
#!/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"
@gregcaporaso
gregcaporaso / cloud_demo_complete.ipynb
Created September 10, 2012 20:06
IPython notebooks corresponding to Reagan et al, ISME Journal 2012
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@gregcaporaso
gregcaporaso / compare_categories.py
Created September 12, 2012 16:58
Patched version of Qiime/scripts/compare_categories.py for QIIME 1.5.0
#!/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"
@gregcaporaso
gregcaporaso / test.txt
Created September 17, 2012 22:15
temp biom file
test
@gregcaporaso
gregcaporaso / gmail.py
Created September 29, 2012 19:07
Functions for sending messages with gmail
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()
@gregcaporaso
gregcaporaso / mapper-comparison-notes.ipynb
Created October 3, 2012 02:23
Comparison of several features of tools for mapping DNA reads to a DNA reference database
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@gregcaporaso
gregcaporaso / README.md
Created October 10, 2012 16:17
Script for running merge_otu_tables.py in parallel

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

@gregcaporaso
gregcaporaso / another_file.md
Created October 15, 2012 21:53
code sprint notes

some other information.