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##GTR lset applyto=() nst=6 # GTR lset applyto=() nst=6 rates=propinv # GTR + I lset applyto=() nst=6 rates=gamma # GTR + gamma lset applyto=() nst=6 rates=invgamma # GTR + I + gamma

##SYM

lset applyto=() nst=6                           # SYM

prset applyto=() statefreqpr=fixed(equal)

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#!/usr/bin/env python
# encoding: utf-8
"""
bed_from_genbank.py

grab the gene records from a genbank file (edit for other record types).

- requires:  biopython

"""

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Proper Setup of Py2App

This assumes you have a proper Framework'd Python installation.

brew install python --framework 

Install Qt v4.7.1

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• TODO: need to check block device mapping flags

• crank up an instance

    ec2-run-instances --key ec2-keypair ami-aa30c7c3 --instance-type=cg1.4xlarge \
    --block-device-mapping '/dev/sdb=ephemeral0' \
    --block-device-mapping '/dev/sdc=ephemeral1'
  

• check for instance status and to get ip address for ssh

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<!-- Juke it, baby, Juke it -->
<gtrModel id="JC69">
	<frequencies>
		<frequencyModel dataType="nucleotide">
			<frequencies>
				<!-- JC69 frequencies are equal -->
				<parameter id="JC69.frequencies" value="0.25 0.25 0.25 0.25"/>
			</frequencies>
		</frequencyModel>
	</frequencies>

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• make sure we map the ephemeral storage to the instance on the instance start. This uses a 64-bit Amazon Linux AMI, which is modeled on Fedora. So, the typical Fedora install commands work (e.g. yum install whatever):

    ec2-run-instances --key keypair ami-74f0061d \
    --instance-type=m2.2xlarge \
    --block-device-mapping '/dev/sda2=ephemeral0' \
    --block-device-mapping '/dev/sda3=ephemeral1'
  

• dont think we actually need them, but i like to have them around, in case we do - they also install glibc.x86_64

yum groupinstall "Development Tools"

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import pdb
from Bio import SeqIO
from Bio import Restriction

seq =  SeqIO.read(open('araTha9/chr5.fas','rU'),'fasta')

for attr,value in Restriction.__dict__.iteritems():
    if not attr.startswith('_'):
        if attr not in ['Restriction', 'RestrictionBatch', 
            'Restriction_Dictionary', 'AllEnzymes', 'Analysis', 'CommOnly', 

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import sys
from Bio import Entrez

def get_taxid(species):
    """to get data from ncbi taxomomy, we need to have the taxid.  we can
    get that by passing the species name to esearch, which will return
    the tax id"""
    species = species.replace(" ", "+").strip()
    search = Entrez.esearch(term = species, db = "taxonomy", retmode = "xml")
    record = Entrez.read(search)

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# setup filter (my require MyNCBI signup) for Angiosperms.  Choose "Browse Filters".  Go to:

Filters » Nucleotide » Properties » Taxonomic Groups » Plants

# select

"Flowering Plants"

# run this query in nucleotide

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# assume the following directory structure where contents of doc/ 
# and source/ are already checked into repo., with the exception 
# of the _build directory (i,e. you can check in _themes or _sources 
# or whatever else).
#
# proj/
#    source/
#    doc/

# remove doc/_build/html if present