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@gregcaporaso
gregcaporaso / mgrast_fnas_to_qiime_fna.py
Created Jul 8, 2012
Script to convert a group of MG-RAST files into a single seqs.fna file for use with QIIME
View mgrast_fnas_to_qiime_fna.py
#!/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 Jul 10, 2012
Script for summarizing barcode error in the 'ultra-deep' ANL sequencing run
View summarize_barcodes.py
#!/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 Jul 20, 2012
Quick-and-dirty script to take combined bl6 file and split it into per-metagenome bl6 files.
View qiime_to_humann.py
#!/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 Sep 10, 2012
IPython notebooks corresponding to Reagan et al, ISME Journal 2012
View cloud_demo_complete.ipynb
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@gregcaporaso
gregcaporaso / compare_categories.py
Created Sep 12, 2012
Patched version of Qiime/scripts/compare_categories.py for QIIME 1.5.0
View compare_categories.py
#!/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 / gmail.py
Created Sep 29, 2012
Functions for sending messages with gmail
View gmail.py
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 Oct 3, 2012
Comparison of several features of tools for mapping DNA reads to a DNA reference database
View mapper-comparison-notes.ipynb
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@gregcaporaso
gregcaporaso / README.md
Created Oct 10, 2012
Script for running merge_otu_tables.py in parallel
View README.md

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

View another_file.md

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