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#! /usr/bin/env python
import sys
import argparse
import copy

import sourmash
from sourmash import sourmash_args
from sourmash.logging import notify, error

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import numpy

# works fine
numpy.array([5, 6, 7, 8], dtype=numpy.uint64)

# fails
numpy.array(set([5, 6, 7, 8]), dtype=numpy.uint64)

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# in a Jupyter notebook, after %pylab inline
# so - not a Python bug, but a pylab/numpy thing

c = collections.Counter()
c['a'] = 5
c['b'] = 3
print('XXX:', sum(c.values()))
print('YYY:', sum([ x for x in c.values() ]))

# gives:

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import sys
import sourmash
sbt = sourmash.load_sbt_index(sys.argv[1])
print(next(iter(sbt.leaves())))

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global_var = 'a global variable'

rule all:
     input:
        "1-foo-hello.txt",
        "2-bar-hello.txt",
        "3-fiz-hello.txt",
        "4-bif-hello.txt"

#

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I spent Tues and Wed over by the Hermitage (downtown St Petersburg) being a tourist. A couple of suggestions for those of you who are here for a few more days and want to do the big tourism spots —

a good itinerary involving the below is,

• hermitage early in the day, before it gets busy
• late lunch at the blini place
• boat trip

Everything below involves a total of about 45 minutes of walking, if you start at the hermitage.

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I spent Tues and Wed over by the Hermitage (downtown St Petersburg) being a tourist. A couple of suggestions for those of you who are here for a few more days and want to do the big tourism spots —

a good itinerary involving the below is,

* hermitage early in the day, before it gets busy
* late lunch at the blini place
* boat trip

Everything below involves a total of about 45 minutes of walking, if you start at the hermitage.

ctb

#! /usr/bin/env python
"""
Usage:

python -m screed db <sequencefile>
python extract-screed.py <list of names> <sequencefile>
"""
import argparse, screed, sys

def main():

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Implement contig contamination analysis as in (blog post)

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*~
*.pyc
.sbt.delmont31/
.sbt.subs1/
.sbt.subs2/
.sbt.tully31/
delmont-genome-sigs.tar.gz
delmont-genome-sigs/
delmont31.sbt.json
subs1.sbt.json