terrycojones

#!/usr/bin/env python

from __future__ import print_function

import sys
from ete3 import Tree

assert len(sys.argv) == 2, ('Usage: %s tree-file' % sys.argv[0])

print(Tree(sys.argv[1]).write(format=1))

terrycojones

#!/usr/bin/env python

from __future__ import print_function, division

from math import pi

best = []
bestError = 1e6

for front in range(20, 55):

terrycojones

WARNING: Unable to find `/docs/papers/lipkin-VirCapSeq-VERT-2015.pdf`, skipping url replacement.
CRITICAL: RuntimeError: Warning encountered
Traceback (most recent call last):
  File "/Users/terry/.virtualenvs/dmp3/bin/pelican", line 11, in <module>
    sys.exit(main())
  File "/Users/terry/.virtualenvs/dmp3/lib/python3.6/site-packages/pelican/__init__.py", line 487, in main
    pelican.run()
  File "/Users/terry/.virtualenvs/dmp3/lib/python3.6/site-packages/pelican/__init__.py", line 179, in run
    p.generate_output(writer)
  File "/Users/terry/.virtualenvs/dmp3/lib/python3.6/site-packages/pelican/generators.py", line 600, in generate_output

terrycojones

WARNING: Unable to find `/docs/papers/lipkin-VirCapSeq-VERT-2015.pdf`, skipping url replacement.
CRITICAL: RuntimeError: Warning encountered

terrycojones

#!/usr/bin/env python

from __future__ import print_function, division

import sys
import argparse
import matplotlib.pyplot as plt

parser = argparse.ArgumentParser(
    formatter_class=argparse.ArgumentDefaultsHelpFormatter,

terrycojones

"My dear fellow," Burlingame said caustically, "we sit on a blind rock
careening through space; we are all of us rushing headlong to the
grave. Think you the worms will care, when anon they make a meal of
you, whether you spent your moment sighing wigless in your chamber, or
sacked the golden towns of Montezuma? Lookee, the day's nigh spent;
'tis gone careening into time forever. Not a tale's length since we
lined our bowels with dinner, and already they growl for more. We are
dying men Ebenezer: i'faith, there's time for nought but bold
resolves!"

terrycojones

#!/bin/bash

case $# in
    1|2) ;;
    *) echo "Usage: $(basename $0) year1 [year2]" >&2; exit 1;;
esac

offset=$(($(date "+%Y") - 1950))

case $(basename $0) in

terrycojones

#!/usr/bin/env python

from __future__ import print_function

from dark.diamond.alignments import DiamondReadsAlignments
from dark.fasta import FastaReads

reads = FastaReads('reads.fasta')
readsAlignments = DiamondReadsAlignments(reads, ['out.json.bz2'])

terrycojones

# Iron
^DA\d red
.*_DA\d red

# Bronze
^RISE\d blue
.*_RISE\d blue

terrycojones

250 buffers open, in 20 distinct modes

72                   sh ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
47               python +++++++++++++++++++++++++++++++++++++++++++++++
40                dired ++++++++++++++++++++++++++++++++++++++++
32          fundamental ++++++++++++++++++++++++++++++++
21             markdown +++++++++++++++++++++
10       makefile-gmake ++++++++++
 7                 json +++++++
 6                  org ++++++