| #! /usr/bin/env python | |
| import sys | |
| import argparse | |
| import copy | |
| import sourmash | |
| from sourmash import sourmash_args | |
| from sourmash.logging import notify, error |
| import numpy | |
| # works fine | |
| numpy.array([5, 6, 7, 8], dtype=numpy.uint64) | |
| # fails | |
| numpy.array(set([5, 6, 7, 8]), dtype=numpy.uint64) |
| # 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: |
| import sys | |
| import sourmash | |
| sbt = sourmash.load_sbt_index(sys.argv[1]) | |
| print(next(iter(sbt.leaves()))) |
| global_var = 'a global variable' | |
| rule all: | |
| input: | |
| "1-foo-hello.txt", | |
| "2-bar-hello.txt", | |
| "3-fiz-hello.txt", | |
| "4-bif-hello.txt" | |
| # |
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,
Everything below involves a total of about 45 minutes of walking, if you start at the hermitage.
| 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. |
| #! /usr/bin/env python | |
| """ | |
| Usage: | |
| python -m screed db <sequencefile> | |
| python extract-screed.py <list of names> <sequencefile> | |
| """ | |
| import argparse, screed, sys | |
| def main(): |
Implement contig contamination analysis as in (blog post)
| *~ | |
| *.pyc | |
| .sbt.delmont31/ | |
| .sbt.subs1/ | |
| .sbt.subs2/ | |
| .sbt.tully31/ | |
| delmont-genome-sigs.tar.gz | |
| delmont-genome-sigs/ | |
| delmont31.sbt.json | |
| subs1.sbt.json |